Examples : samtools, bed, topic:conversion

1533 tool(s) found

Tool Description Topics Available version(s)
AEGeAn CanonGFF3 pre-process GFF3 files, removing all features not directly related to protein-coding genes Genome annotation 1
2D Feature Extraction Feature Extraction 3
ABRicate Mass screening of contigs for antimicrobial and virulence genes Antimicrobial resistance prediction 9
ABRicate List List all of abricate's available databases. Antimicrobial resistance prediction 9
ABRicate Summary Combine ABRicate results into a simple matrix of gene presence/absence Antimicrobial resistance prediction 1
ABySS de novo sequence assembler 9
Add column to an existing dataset Editing 2
Add LoFreq alignment quality scores to aligned read SAM/BAM records 4
Add metadata to a BIOM table Conversion Format validation 8
AddCommentsToBam add comments to BAM dataset 14
AddOrReplaceReadGroups add or replaces read group information 14
AEGeAn GAEVAL compute coverage and integrity scores for gene models using transcript alignments. Genome annotation 1
AEGeAn LocusPocus calculate locus coordinates for the given gene annotation Genome annotation 1
AEGeAn ParsEval compare two sets of gene annotations for the same sequence. Genome annotation 1
Aggregate datapoints Appends the average, min, max of datapoints per interval 2
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 12
Align.check Calculate the number of potentially misaligned bases 6
Align.seqs Align sequences to a template alignment 5
alimask append modelmask line to a multiple sequence alignments 7
Amino Acid Coverage Builds an aa census and returns its coverage 2
Amino Acid Variants Identifies amino acid mutations 2
Amova Analysis of molecular variance 5
Analyse canonical genes against 'peak' data using RnaChipIntegrator 3
AnnData Operations modifies metadata and flags genes 13
Annotate DESeq2/DEXSeq output tables Append annotation from GTF to differential expression tool outputs 2
annotateMyIDs annotate a generic set of identifiers 11
Anosim Non-parametric multivariate analysis of changes in community structure 5
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 5
Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters 7
ASTRAL-III. Tool for estimating an unrooted species tree given a set of unrooted gene trees. 1
Augustus gene prediction for prokaryotic and eukaryotic genomes 8
Auto Threshold applies a standard threshold algorithm to an image 3
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment Conversion 1
AXT to FASTA Converts an AXT formatted file to FASTA format Conversion 1
AXT to LAV Converts an AXT formatted file to LAV format Conversion 1
backtranseq Back translate a protein sequence 7
Bakta genome annotation via alignment-free sequence identification 2
BAM filter Removes reads from a BAM file based on criteria 4
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 10
bam-to-bai converter 1
BAM-to-SAM convert BAM to SAM 5
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 10
bamCompare normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them 16
bamCoverage generates a coverage bigWig file from a given BAM or CRAM file 18
BamLeftAlign indels in BAM datasets 12
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 16
BamUtil diff two coordinate sorted SAM/BAM files Sequence cutting 1
banana Bending and curvature plot in B-DNA 5
Bandage Image visualize de novo assembly graphs 8
Bandage Info determine statistics of de novo assembly graphs 6
Bar chart for multiple columns 2
Barcode Splitter 4
barrnap Locate ribosomal RNA's in a fasta file. (GFF output) 4
Base Coverage of all intervals Quantification 5
Batch_correction Corrects intensities for signal drift and batch-effects 4
BBTools: BBduk decontamination using kmers Global alignment Pairwise sequence alignment 3
bcf_uncompressed-to-bcf converter 1
bcftools annotate Annotate and edit VCF/BCF files 11
bcftools call SNP/indel variant calling from VCF/BCF 12
bcftools cnv Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values 14
bcftools concat Concatenate or combine VCF/BCF files 10
bcftools consensus Create consensus sequence by applying VCF variants to a reference fasta file 13
bcftools convert from vcf Converts VCF/BCF to IMPUTE2/SHAPEIT formats 10
bcftools convert to vcf Converts other formats to VCF/BCFk 10
bcftools counts plugin counts number of samples, SNPs, INDELs, MNPs and total sites 11
bcftools csq Haplotype aware consequence predictor 11
bcftools dosage plugin genotype dosage 10
bcftools fill-AN-AC plugin Fill INFO fields AN and AC 10
bcftools fill-tags plugin Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi 10
bcftools filter Apply fixed-threshold filters 10
bcftools fixploidy plugin Fix ploidy 10
bcftools gtcheck Check sample identity 10
bcftools impute-info plugin Add imputation information metrics to the INFO field 10
bcftools isec Create intersections, unions and complements of VCF files 11
bcftools List Samples in VCF/BCF file 10
bcftools mendelian plugin Count Mendelian consistent / inconsistent genotypes 10
bcftools merge Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file 11
bcftools missing2ref plugin Set missing genotypes 10
bcftools mpileup Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files 11
bcftools norm Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows 13
bcftools query Extracts fields from VCF/BCF file and prints them in user-defined format 11
bcftools reheader Modify header of VCF/BCF files, change sample names 10
bcftools roh HMM model for detecting runs of homo/autozygosity 10
bcftools setGT plugin Sets genotypes 10
bcftools stats Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats 12
bcftools tag2tag plugin Convert between similar tags, such as GL and GP 12
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 14
bed to protein map genomic location of proteins for MVP 2
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BedCov calculate read depth for a set of genomic intervals 5
bedgraph-to-bigwig converter 1
BedToIntervalList convert coordinate data into picard interval list format 14
bedtools AnnotateBed annotate coverage of features from multiple files 21
bedtools BAM to BED converter 23
bedtools BED to BAM converter 21
bedtools BED to IGV create batch script for taking IGV screenshots 16
bedtools BED12 to BED6 converter 20
bedtools BEDPE to BAM converter 21
bedtools ClosestBed find the closest, potentially non-overlapping interval 21
bedtools ClusterBed cluster overlapping/nearby intervals 20
bedtools ComplementBed Extract intervals not represented by an interval file 21
bedtools ExpandBed replicate lines based on lists of values in columns 20
bedtools FisherBed calculate Fisher statistic between two feature files 20
bedtools FlankBed create new intervals from the flanks of existing intervals 21
bedtools Genome Coverage compute the coverage over an entire genome 20
bedtools GroupByBed group by common cols and summarize other cols 20
bedtools JaccardBed calculate the distribution of relative distances between two files 20
bedtools LinksBed create a HTML page of links to UCSC locations 20
bedtools MakeWindowsBed make interval windows across a genome 21
bedtools MaskFastaBed use intervals to mask sequences from a FASTA file 20
bedtools Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 20
bedtools MergeBED combine overlapping/nearby intervals into a single interval 20
bedtools MultiCovBed counts coverage from multiple BAMs at specific intervals 20
bedtools Multiple Intersect identifies common intervals among multiple interval files 23
bedtools OverlapBed computes the amount of overlap from two intervals 20
bedtools RandomBed generate random intervals in a genome 21
bedtools ReldistBed calculate the distribution of relative distances 20
bedtools ShuffleBed randomly redistrubute intervals in a genome 21
bedtools SlopBed adjust the size of intervals 22
bedtools SortBED order the intervals 20
bedtools SpacingBed reports the distances between features 17
bedtools SubtractBed remove intervals based on overlaps 20
bedtools TagBed tag BAM alignments based on overlaps with interval files 20
bedtools WindowBed find overlapping intervals within a window around an interval 20
Berokka Trim, circularise, orient and filter long read bacterial genome assemblies 1
bigwig-to-wig converter 1
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
Bin.seqs Order Sequences by OTU 5
Binary 2 Label Converts Binary to Label Image 2
Biom.info create shared and taxonomy files from biom 2
biom2-to-biom1 converter 1
Bionano Hybrid Scaffold automates the scaffolding process Genome assembly 7
biosed Replace or delete sequence sections 5
biosyntheticSPAdes biosynthetic gene cluster assembly 6
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 18
BlastXML to gapped GFF3 1
blockbuster detects blocks of overlapping reads using a gaussian-distribution approach 3
BlockClust efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles 2
Bowtie2 - map reads against reference genome 21
Boxplot of quality statistics 2
breseq find mutations in haploid microbial genomes DNA mapping Genetic mapping Genome annotation Mapping assembly Protein SNP mapping Sequence word comparison 4
btwisted Calculates the twisting in a B-DNA sequence 5
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 12
Bundle Collection Download a collection of files 2
Busco assess genome assembly and annotation completeness 15
BWA-MEM2 - map medium and long reads (> 100 bp) against reference genome 1
bwameth Fast and accurate aligner of BS-Seq reads. 6
Cactus whole-genome multiple sequence alignment 7
Cactus: export whole-genome multiple sequence alignment to other formats 9
cai CAI codon adaptation index 5
cai custom CAI codon adaptation index using custom codon usage file 5
Calculate a Heinz score for each node 2
Calculate community metrics calculate community metrics from abundance data 3
Calculate presence absence table calculate presence absence table from observation data 3
Calculate the box parameters using RDKit for an AutoDock Vina job from a ligand or pocket input file (confounding box) 5
Call and phase heterozygous SNPs 4
Call variants with LoFreq 7
CAMERA.annotate CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 9
CAMERA.combinexsAnnos Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations. 9
Canu assembler Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore 4
cap3 Sequence Assembly tool DNA mapping Mapping Mapping assembly Sequence assembly 2
CAT bins annotate with taxonomic classification 2
CAT summarise the number of contigs or bins assigned to each taxonomic name 1
Categorize by collapsing hierarchical data to a specified functional level 2
Categorize Elements satisfying criteria 1
CD-HIT PROTEIN Cluster a protein dataset into representative sequences 3
CD-HIT-EST Cluster a nucleotide dataset into representative sequences 3
CellProfiler run a CellProfiler pipeline 2
Change Case of selected columns 2
chaos Create a chaos game representation plot for a sequence 5
charge Protein charge plot 5
Check Format Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files 2
checktrans Reports STOP codons and ORF statistics of a protein 5
ChEMBL structure pipeline for curation and standardizing of molecular structures 2
Chimera.bellerophon Find putative chimeras using bellerophon 5
Chimera.ccode Find putative chimeras using ccode 6
Chimera.check Find putative chimeras using chimeraCheck 5
Chimera.perseus Find putative chimeras using chimeraCheck 6
Chimera.pintail Find putative chimeras using pintail 5
Chimera.slayer Find putative chimeras using slayer 5
Chimera.uchime Find putative chimeras using uchime 5
Chimera.vsearch find potential chimeric sequences using vsearch 4
chips Codon usage statistics 5
ChIPseeker for ChIP peak annotation and visualization 6
Chop.seqs Trim sequences to a specified length 6
Chromeister ultra-fast pairwise genome comparisons 5
CIRCexplorer 2
Circos visualizes data in a circular layout Visualisation 11
Circos Builder creates circos plots from standard bioinformatics datatypes. 2
Circos: Alignments to links reformats alignment files to prepare for Circos Parsing 10
Circos: bigWig to Scatter reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots Conversion 10
Circos: Bundle Links reduce numbers of links in datasets before plotting Aggregation 10
Circos: Interval to Circos Text Labels reformats interval files to prepare for Circos text labels Conversion 10
Circos: Interval to Tiles reformats interval files to prepare for Circos tile plots Conversion 10
Circos: Link Density Track reduce links to a density plot Aggregation 10
Circos: Resample 1/2D data reduce numbers of points in a dataset before plotting Aggregation 10
Circos: Stack bigWigs as Histogram reformats for use in Circos stacked histogram plots Formatting 6
Circos: Table viewer easily creates circos plots from tabular data Visualisation 10
cirdna Draws circular maps of DNA constructs 5
Classify.otu Assign sequences to taxonomy 5
Classify.rf description 2
Classify.seqs Assign sequences to taxonomy 5
Classify.tree Get a consensus taxonomy for each node on a tree 5
CleanSam perform SAM/BAM grooming 14
Clearcut Generate a tree using relaxed neighbor joining 5
CLIFinder Find chimerics transcripts containing LINEs sequences 1
climate stripes from timeseries Visualisation 3
clinker Automatic creation of publication-ready gene cluster comparison figures 1
Clip adapter sequences 6
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 10
ClustalW multiple sequence alignment program for DNA or proteins 5
Cluster Assign sequences to OTUs (Operational Taxonomic Unit) 4
Cluster the intervals of a dataset Sequence clustering Sequence merging 5
Cluster Inspection using RaceID examines gene expression within clusters 6
Cluster, infer trajectories and embed with scanpy 7
Cluster.classic Assign sequences to OTUs (Dotur implementation) 5
Cluster.fragments Group sequences that are part of a larger sequence 5
Cluster.split Assign sequences to OTUs and split large matrices 5
Clustering using RaceID performs clustering, outlier detection, dimensional reduction 6
cmalign Align sequences to a covariance model against a sequence database 3
cmbuild Build covariance models from sequence alignments 4
cml-to-mol2 converter 1
cml-to-smi converter 2
cmpress Prepare a covariance model database for cmscan 2
cmscan Search sequences against collections of covariance models 2
cmsearch Search covariance model(s) against a sequence database 3
cmstat Summary statistics for covariance model 3
codcmp Codon usage table comparison 5
coderet Extract CDS, mRNA and translations from feature tables 5
Codon Variants Identifies codon variants and non-synonymous/synonymous mutations 2
Collapse sequences 3
Collapse Collection into single dataset in order of the collection 5
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 14
Collect.shared Generate collector's curves for calculators on OTUs 5
Collect.single Generate collector's curves for OTUs 6
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 14
CollectGcBiasMetrics charts the GC bias metrics 14
CollectHsMetrics compute metrics about datasets generated through hybrid-selection (e.g. exome) 4
CollectInsertSizeMetrics plots distribution of insert sizes 14
Collector’s curve of sequencing yield over time 2
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 15
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 14
ColorToGray converts color and channel-stacked images to grayscale 2
Column arrange by header name 2
Column Join on Collections 5
Column Regex Find And Replace 6
Combine FASTA and QUAL into FASTQ Aggregation 5
Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances 3
Compare BIOM tables Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples. 3
Compare two Datasets to find common or distinct rows Filtering 1
Complement intervals of a dataset Sequence coordinate conversion 6
Complexity BAM 2
Complexity FASTA 2
Compound conversion - interconvert between various chemistry and molecular modeling data files 6
Compress file(s) 1
compseq Count composition of dimer/trimer/etc words in a sequence 5
Compute on rows 10
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 21
Compute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly 10
Compute GLM on community data Compute a GLM of your choice on community data 2
Compute GLM on population data Compute a GLM of your choice on population data 2
Compute Motif Frequencies in indel flanking regions 2
Compute Motif Frequencies For All Motifs motif by motif 2
Compute P-values and Correlation Coefficients for Feature Occurrences between two datasets using Discrete Wavelet Transfoms 2
Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features between two datasets using Discrete Wavelet Transfoms 2
Compute P-values and Max Variances for Feature Occurrences in one dataset using Discrete Wavelet Transfoms 2
Compute P-values and Second Moments for Feature Occurrences between two datasets using Discrete Wavelet Transfoms 2
Compute quality statistics 3
Compute sequence length 6
computeGCBias Determine the GC bias of your sequenced reads 17
computeMatrix prepares data for plotting a heatmap or a profile of given regions 18
computeMatrixOperations Modify or combine the output of computeMatrix in a variety of ways. 11
Concatenate FASTA alignment by species 3
Concatenate two BED files Aggregation 6
Concatenate datasets tail-to-head Aggregation 1
Concatenate datasets tail-to-head (cat) 11
Concatenate multiple datasets tail-to-head 1
Concatenate multiple datasets tail-to-head 4
Condense consecutive characters 2
Consensus Sequence Generate a consensus sequence from a BAM file 2
Consensus.seqs Find a consensus sequence for each OTU or phylotype 6
ConsensusID Computes a consensus of peptide identifications of several identification engines. 6
Construct Expression Set Object Create an ExpressionSet object from tabular and textual data 5
Convert delimiters to TAB 1
Convert between BIOM table formats 9
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 2
Convert FASTA to Bowtie color space Index 2
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert from BAM to FastQ 13
Convert genome coordinates between assemblies and genomes 2
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 2
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 2
Convert GFF to BED 2
Convert GFF to Feature Location Index 1
Convert GFF3 to prot_table for TRANSIT 4
Convert gffCompare annotated GTF to BED for StringTie results 4
Convert GTF to BED12 1
Convert image Convert image 2
Convert Kraken data to Galaxy taxonomy representation 3
Convert Len file to Linecount 2
Convert lped to fped 2
Convert lped to plink pbed 2
Convert MAF to Fasta 2
Convert MAF to Genomic Intervals 2
Convert Picard Interval List to BED6 converter 2
Convert plink pbed to ld reduced format 2
Convert plink pbed to linkage lped 2
Convert SAM to interval 2
Convert VCF to MAF with vcf2maf 3
ConvertObjectsToImage convert the identified objects into an image 2
Cooccurrence tests whether presence-absence patterns differ from chance 6
Copernicus Climate Data Store for retrieveing climate data Data retrieval Format detection Formatting 1
coronaSPAdes SARS-CoV-2 de novo genome assembler 6
Corr.axes correlation of data to axes 5
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Correlation for numeric columns 1
Cosine Content - measure the cosine content of the PCA projection 4
Count occurrences of each record 2
Count GFF Features 2
Count Objects in labled images 1
Count.groups counts the number of sequences represented by a specific group or set of groups 5
Count.seqs (aka make.table) counts the number of sequences represented by the representative 5
Coverage of a set of intervals on second set of intervals Comparison Filtering 5
cpgplot Plot CpG rich areas 5
cpgreport Reports all CpG rich regions 5
cram-to-bam converter 2
Create a deep learning model architecture using Keras 6
Create a genus level gene families file 4
Create a plot from GLM data as temporal trend 1
Create assemblies with Unicycler pipeline for bacterial genomes Genome assembly 10
Create deep learning model with an optimizer, loss function and fit parameters 6
Create Frankenstein ligand for docking active site definition 3
Create InterMine Interchange Dataset 1
Create nested list based on filenames and batch sizes 2
Create single interval as a new dataset 1
Create text file with recurring lines 9
Create.database creates a database file from a list, repnames, repfasta and contaxonomy file 5
csv-to-tabular converter 1
CTSM/FATES-EMERALD Functionally Assembled Terrestrial Ecosystem Simulator Ecological modelling Modelling and simulation 2
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 8
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cuffmerge merge together several Cufflinks assemblies 8
Cuffnorm Create normalized expression levels 7
Cuffquant Precompute gene expression levels 4
cummeRbund visualize Cuffdiff output 3
cusp Create a codon usage table 5
CustomProDB Generate protein FASTAs from exosome or transcriptome data 2
Cut columns from a table Filtering 2
Cut columns from a table (cut) 9
cut_francais keep or remove selected column 1
Cutadapt Remove adapter sequences from FASTQ/FASTA Sequence editing 22
cuteSV detects long-read-based SVs 1
cutseq Removes a specified section from a sequence 5
dada2: assignTaxonomy and addSpecies Learn Error rates 6
dada2: dada Remove sequencing errors 6
dada2: filterAndTrim Filter and trim short read data 6
dada2: learnErrors Learn Error rates 6
dada2: makeSequenceTable construct a sequence table (analogous to OTU table) 6
dada2: mergePairs Merge denoised forward and reverse reads 6
dada2: plotComplexity Plot sequence complexity profile 6
dada2: plotQualityProfile plot a visual summary of the quality scores 6
dada2: removeBimeraDenovo Remove bimeras from collections of unique sequences 6
dada2: sequence counts 6
dan Calculates DNA RNA/DNA melting temperature 5
Data Fetch Query and retrieval 1
Datamash (operations on tabular data) 5
DAVID functional annotation for a list of genes 1
dbnsfp.tabular-to-snpsiftdbnsfp converter 3
DecoyDatabase Create decoy sequence database from forward sequence database. 5
Deep learning training and evaluation conduct deep training and evaluation either implicitly or explicitly 4
Degap.seqs Remove gap characters from sequences 5
degapseq Removes gap characters from sequences 5
Deletion Profile calculates the distributions of deleted nucleotides across reads 6
Delta-Filter Filters alignment (delta) file from nucmer Read mapping Sequence alignment 5
Describe samples and replicates 11
descseq Alter the name or description of a sequence 5
DESeq2 Determines differentially expressed features from count tables Differential gene expression profiling RNA-Seq quantification 22
Determine_batch_correction to choose between linear, lowess and loess methods 4
Deunique.seqs Return all sequences 5
Deunique.tree Reinsert the redundant sequence identiers back into a unique tree. 5
DEXSeq Determines differential exon usage from count tables 10
DEXSeq-Count Prepare and count exon abundancies from RNA-seq data 10
DIA_Umpire_SE DIA signal extraction 1
Diamond alignment tool for short sequences against a protein database Sequence alignment analysis 9
Diamond makedb Build database from a FASTA file Sequence alignment analysis 8
Diamond view generate formatted output from DAA files Sequence alignment analysis 6
diapysef library generation generates spectral library for DIA analysis 1
DiffBind differential binding analysis of ChIP-Seq peak data 12
Differential expression analysis using a Trinity assembly 11
diffseq Find differences between nearly identical sequences 5
digest Protein proteolytic enzyme or reagent cleavage digest 5
DisplayDataOnImage produce an image with data on top of identified objects 2
Dist.seqs calculate uncorrected pairwise distances between aligned sequences 5
Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups 5
DNAdiff Evaluate similarities/differences between two sequences Read mapping Sequence alignment 5
dNdS Report Calculate the dN/dS value for each region in a bed file 2
dotmatcher Displays a thresholded dotplot of two sequences 5
dotpath Non-overlapping wordmatch dotplot of two sequences 5
dottup Displays a wordmatch dotplot of two sequences 5
Download and Extract Reads in BAM format from NCBI SRA Data retrieval Formatting 24
Download and Extract Reads in FASTQ format from NCBI SRA Data retrieval Formatting 20
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
dpocket to calculate descriptors for protein pockets 1
Draw nucleotides distribution chart 4
Draw quality score boxplot 4
Draw ROC plot on "Perform LDA" output 2
Draw Stacked Bar Plots for different categories and different criteria 1
dreg Regular expression search of a nucleotide sequence 6
DropletUtils Utilities for handling droplet-based single-cell RNA-seq data DNA barcoding Parsing 9
Drug Resistance Mutations 2
edgeR Perform differential expression of count data Differential gene expression profiling RNA-seq read count analysis 10
edgeR-repenrich Determines differentially expressed features from RepEnrich counts 1
eggNOG Mapper functional sequence annotation by orthology 10
EGSEA easy and efficient ensemble gene set testing 4
einverted Finds DNA inverted repeats 5
ENA Upload tool 9
EncyclopeDIA Library Searching Directly from Data-Independent Acquisition (DIA) MS/MS Data 3
EncyclopeDIA Quantify samples from Data-Independent Acquisition (DIA) MS/MS Data 3
EnhanceOrSuppressFeatures to improve subsequent identification of objects 2
Ensemble methods for classification and regression 12
Enumerate changes calculated with Dimorphite DL and RDKit 2
epestfind Finds PEST motifs as potential proteolytic cleavage sites 5
equicktandem Finds tandem repeats 5
est2genome Align EST and genomic DNA sequences 5
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
Estimator attributes get important attributes from an estimator or scikit object 9
etandem Looks for tandem repeats in a nucleotide sequence 5
Exonerate pairwise sequence comparison 4
Export datasets to remote files source 1
Export to GraPhlAn 2
ExportToSpreadsheet export measurements into one or more files 2
eXpress Quantify the abundances of a set of target sequences from sampled subsequences 2
Extract and cluster differentially expressed transcripts from a Trinity assembly 12
Extract element identifiers of a list collection 2
Extract energy components with GROMACS 7
Extract FASTQ in tabular format from a set of FAST5 files 2
Extract features from GFF data 1
Extract MAF blocks given a set of genomic intervals 4
Extract MAF by block number given a set of block numbers and a MAF file 1
Extract nanopore events from a set of sequencing reads 2
Extract Pairwise MAF blocks given a set of genomic intervals 1
Extract reads in FASTA or FASTQ format from nanopore files 2
Extract time and channel information from a set of FAST5 files 2
Extract values from an SD-file into a tabular file using RDKit 4
extractfeat Extract features from a sequence 5
extractseq Extract regions from a sequence 5
FalseDiscoveryRate Estimates the false discovery rate on peptide and protein level using decoy searches. 7
faSplit Split a FASTA file 3
Fasta Extract Sequence Extract a single sequence from a fasta file. 2
FASTA Merge Files and Filter Unique Sequences Concatenate FASTA database files together 4
Fasta Statistics Display summary statistics for a fasta file. 5
FASTA Width formatter 3
fasta-to-fai converter 1
FASTA-to-Tabular converter 3
FastaCLI Appends decoy sequences to FASTA files 6
Faster Download and Extract Reads in FASTQ format from NCBI SRA Data retrieval Formatting 15
fastp - fast all-in-one preprocessing for FASTQ files 8
FASTQ de-interlacer on paired end reads Splitting 5
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 5
FASTQ interlacer on paired end reads Aggregation 6
FASTQ joiner on paired end reads Aggregation 7
FASTQ Masker by quality score Sequence masking 5
FASTQ Quality Trimmer by sliding window 5
FASTQ splitter on joined paired end reads Splitting 6
FASTQ Summary Statistics by column Sequence assembly validation 4
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 6
FASTQ to FASTA converter Conversion 5
FASTQ to Tabular converter Sequence conversion 5
FASTQ Trimmer by column Sequence trimming 5
Fastq.info Convert fastq to fasta and quality 6
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
FASTQE visualize fastq files with emoji's 🧬😎 5
fastqillumina-to-fqtoc converter 1
FastqToSam convert Fastq data into unaligned BAM 19
FASTTREE build maximum-likelihood phylogenetic trees Phylogenetic analysis Phylogenetic inference (from molecular sequences) 4
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 25
FeatureFinderMultiplex Determination of peak ratios in LC-MS data 7
Fetch closest non-overlapping feature for every interval Filtering 4
fgsea - fast preranked gene set enrichment analysis 3
FidoAdapter Runs the protein inference engine Fido. 6
FileConverter Converts between different MS file formats. 5
FileFilter Extracts or manipulates portions of data from peak, feature or consensus-feature files. 5
FileInfo Shows basic information about the file, such as data ranges and file type. 5
FileMerger Merges several MS files into one file. 5
Filter data on any column using simple expressions Formatting 2
Filter with scanpy 7
Filter and merge chimeric reads from Arima Genomics 1
Filter BAM datasets on a variety of attributes 6
Filter by quality Filtering 6
Filter Combined Transcripts using tracking file 1
Filter FASTA on the headers and/or the sequences 5
Filter FASTQ reads by quality score and length Filtering 4
Filter GFF data by attribute using simple expressions 2
Filter GFF data by feature count using simple expressions 1
Filter GTF data by attribute values_list 2
Filter Image applies a standard filter to an image 2
Filter low expression transcripts from a Trinity assembly 11
Filter MAF by specified attributes 1
Filter MAF blocks by Species 1
Filter MAF blocks by Size 1
Filter pileup on coverage and SNPs 3
Filter SAM on bitwise flag values 1
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 6
Filter segmentation Filter segmentation by rules 1
Filter sequences by ID from a tabular file 5
Filter sequences by length Filtering 6
Filter Tabular 5
Filter with SortMeRNA of ribosomal RNAs in metatranscriptomic data 6
Filter.seqs removes columns from alignments 5
Filter.shared remove OTUs based on various critieria 6
FilterSamReads include or exclude aligned and unaligned reads and read lists 14
filtlong Filtering long reads by quality 3
Finds SNP sites from a multi-FASTA alignment file 1
Fit a BUM model with p-values 2
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 14
FlashLFQ ultrafast label-free quantification for mass-spectrometry proteomics 5
Flye de novo assembler for single molecule sequencing reads Genome assembly 8
Format tree and trait tables 2
Format MetaPhlAn2 output for Krona 2
FPKM Count calculates raw read count, FPM, and FPKM for each gene 8
fpocket - find potential binding sites in protein structures 4
FragGeneScan for finding (fragmented) genes in short reads 2
freak Residue/base frequency table or plot 5
FreeBayes bayesian genetic variant detector 12
Funannotate assembly clean 5
Funannotate compare annotations 5
Funannotate functional annotation 5
Funannotate predict annotation 6
fuzznuc Nucleic acid pattern search 6
fuzzpro Protein pattern search 5
fuzztran Protein pattern search after translation 5
g:Profiler tools for functional profiling of gene lists 1
garnier Predicts protein secondary structure 5
Gblocks Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Sequence masking 3
GC Skew calculates skew over genomic sequences Nucleic acid property calculation 10
Gecko Ungapped genome comparison 3
geecee Calculates fractional GC content of nucleic acid sequences 5
GEMINI actionable_mutations Retrieve genes with actionable somatic mutations via COSMIC and DGIdb 4
GEMINI amend Amend an already loaded GEMINI database. 5
GEMINI annotate the variants in an existing GEMINI database with additional information 7
GEMINI autosomal recessive/dominant Find variants meeting an autosomal recessive/dominant model 2
GEMINI burden perform sample-wise gene-level burden calculations 4
GEMINI comp_hets Identifying potential compound heterozygotes 2
GEMINI database info Retrieve information about tables, columns and annotation data stored in a GEMINI database 4
GEMINI de_novo Identifying potential de novo mutations 2
GEMINI dump Extract data from the Gemini DB 2
GEMINI fusions Identify somatic fusion genes from a GEMINI database 5
GEMINI gene_wise Custom genotype filtering by gene 5
GEMINI inheritance pattern based identification of candidate genes 2
GEMINI interactions Find genes among variants that are interacting partners 4
GEMINI load Loading a VCF file into GEMINI 7
GEMINI lof_sieve Filter LoF variants by transcript position and type 4
GEMINI mendel_errors Identify candidate violations of Mendelian inheritance 2
GEMINI pathways Map genes and variants to KEGG pathways 5
GEMINI qc Quality control tool 5
GEMINI query Querying the GEMINI database 5
GEMINI region Extracting variants from specific regions or genes 2
GEMINI roh Identifying runs of homozygosity 5
GEMINI set_somatic Tag somatic mutations in a GEMINI database 5
GEMINI stats Compute useful variant statistics 4
GEMINI windower Conducting analyses on genome "windows" 4
Genbank to GFF3 converter 2
Genbank-to-Fasta produces a Fasta file from a genbank file 1
genbank-to-genbank.gz converter 1
genbank.gz-to-genbank converter 1
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 13
Gene Body Coverage (Bigwig) Read coverage over gene body 12
Gene length and GC content from GTF and FASTA file 4
Generalized linear models for classification and regression 11
Generate A Matrix for using PC and LDA 1
Generate box-whisker plot of quality score distribution over positions in nanopore reads 2
Generate count matrix from individual files 1
Generate gene to transcript map for Trinity assembly 10
Generate histogram of nanopore read lengths 2
Generate MD topologies for small molecules using acpype 9
Generate pileup from BAM dataset 3
Generation, personalization and annotation of tree for GraPhlAn 2
Generic_Filter Removes elements according to numerical or qualitative values 3
Genome annotation statistics 1
GenomeScope reference-free genome profiling 3
Genrich Detecting sites of genomic enrichment 3
Get flanks returns flanking region/s for every gene Sequence analysis 4
Get longest read from a set of FAST5 files. 2
Get open reading frames (ORFs) or coding sequences (CDSs) e.g. to get peptides from ESTs 5
Get organelle from reads 1
Get PDB file from Protein Data Bank 2
Get.communitytype description 5
Get.coremicrobiome fraction of OTUs for samples or abundances 6
Get.dists selects distances from a phylip or column file 5
Get.group group names from shared or from list and group 6
Get.groups Select groups 5
Get.label label names from list, sabund, or rabund file 5
Get.lineage Picks by taxon 6
Get.mimarkspackage creates a mimarks package form with your groups 5
Get.otulabels Selects OTU labels 6
Get.otulist Get otus for each distance in a otu list 5
Get.oturep Generate a fasta with a representative sequence for each OTU 5
Get.otus Get otus containing sequences from specified groups 5
Get.rabund Get rabund from a otu list or sabund 6
Get.relabund Calculate the relative abundance of each otu 5
Get.sabund Get sabund from a otu list or rabund 5
Get.seqs Picks sequences by name 5
Get.sharedseqs Get shared sequences at each distance from list and group 5
GetFastaBed use intervals to extract sequences from a FASTA file 20
getorf Finds and extracts open reading frames (ORFs) 5
GFA to FASTA Convert Graphical Fragment Assembly files to FASTA format 4
gfastats the swiss army knife for genome assembly 8
GFF-to-BED converter Conversion 1
gff3.bz2-to-gff3 converter 1
GffCompare compare assembled transcripts to a reference annotation 5
gffread Filters and/or converts GFF3/GTF2 records 7
GMAJ Multiple Alignment Viewer 1
GOEnrichment performs GO enrichment analysis of a set of gene products 2
goseq tests for overrepresented gene categories Gene-set enrichment analysis 12
GOSlimmer converts a set of annotation from GO to a given GOSlim version 2
GraPhlAn to produce graphical output of an input tree 2
GrayToColor take grayscale images and produces a color image from them 2
gro-to-pdb converter 1
GROMACS energy minimization of the system prior to equilibration and production MD 7
GROMACS initial setup of topology and GRO structure file 6
GROMACS simulation for system equilibration or data collection 9
GROMACS solvation and adding ions to structure and topology files 8
GROMACS structure configuration using editconf 5
Group data by a column and perform aggregate operation on other columns. 4
GTDB-Tk Classify genomes by placement in GTDB reference tree 1
GTF-to-BEDGraph converter Conversion 1
gtf-to-interval_index converter 1
GTF2GeneList extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer 6
Gubbins Recombination detection in Bacteria 2
Gumbel - determine essential genes 6
Hapcut2 - haplotype assembly for diploid organisms 1
Hcluster Assign sequences to OTUs (Operational Taxonomic Unit) 2
Heatmap w ggplot 6
Heatmap.bin Generate a heatmap for OTUs 5
Heatmap.sim Generate a heatmap for pariwise similarity 5
heatmap2 6
helixturnhelix Report nucleic acid binding motifs 5
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 6
hicBuildMatrix create a contact matrix 18
hicFindTADs identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin 16
hicMergeMatrixBins merge adjacent bins from a Hi-C contact matrix to reduce its resolution 15
hicPCA compute the principal components for A / B compartment analysis 12
hicPlotMatrix plot a Hi-C contact matrix heatmap 16
HiFi Adapter Filter Remove CCS reads with remnant PacBio adapter sequences 1
Hifiasm haplotype-resolved de novo assembler for PacBio Hifi reads 11
Hifiasm_meta for metagenome assembly using Hifi reads 2
HighResPrecursorMassCorrector Corrects the precursor mass and charge determined by the instrument software. 5
HISAT2 A fast and sensitive alignment program 19
Histogram of a numeric column 4
Histogram equalization automatic histogram equalization 1
HMDB MS search search by masses on HMDB online LCMS bank 6
hmmalign align sequences to a profile HMM 7
hmmbuild Build a profile HMM from an input multiple alignment 8
hmmconvert convert profile file to a HMMER format 7
hmmemit sample sequence(s) from a profile HMM 7
hmmfetch retrieve profile HMM(s) from a file 7
hmmscan search sequence(s) against a profile database 8
hmmsearch search profile(s) against a sequence database 8
hmoment Hydrophobic moment calculation 5
Homova Homogeneity of molecular variance 5
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
HUMAnN to profile presence/absence and abundance of microbial pathways and gene families Nucleic acid sequence analysis Phylogenetic analysis 2
HUMAnN2 to profile presence/absence and abundance of microbial pathways and gene families 5
Hydra pipeline Identifies drug resistance within an NGS dataset 2
Hydrogen Bond Analysis using VMD between two segments of a trajectory 1
Hyperparameter Search performs hyperparameter optimization using various SearchCVs 11
HyPhy-aBSREL adaptive Branch Site Random Effects Likelihood 27
HyPhy-GARD Genetic Algorithm for Recombination Detection 26
IDConflictResolver Resolves ambiguous annotations of features with peptide identifications 5
Identification Parameters Sets the identification parameters to be used in SearchGUI and PeptideShaker apps 6
Identify optimal scoring subnetwork using Heinz 2
IdentifyPrimaryObjects identify biological objects of interest 2
IDFilter Filters results from protein or peptide identification engines based on different criteria. 6
IDMapper Assigns protein/peptide identifications to features or consensus features. 5
IDMerger Merges several protein/peptide identification files into one file. 6
IDPosteriorErrorProbability Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. 5
IDScoreSwitcher Switches between different scores of peptide or protein hits in identification data 6
IdxStats reports stats of the BAM index file 8
iep Calculates the isoelectric point of a protein 5
Illuminapairedend - Assembling pair-end reads Construct consensus reads from Illumina pair-end reads 3
Image Info Show Image Info 2
ImageMath perform simple mathematical operations on images 2
Import Anndata and loom from different format 9
inchi-to-mol converter 2
Indicator Identify indicator "species" for nodes on a tree 5
Infer Experiment speculates how RNA-seq were configured 12
infoseq Displays some simple information about sequences 5
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 12
Insert indel qualities into a BAM file 4
Insertion Profile calculates the distribution of inserted nucleotides across reads 6
Inspect and manipulate with scanpy 7
Inspect AnnData object 10
Inspect Expression Set Object Inspect an ExpressionSet object by a variety of attributes 5
Integron Finder is a program that detects integrons in DNA sequences Genome annotation Nucleic acid sequence feature detection Protein sequence feature detection Sequence motif recognition 2
InterProphet Combine Peptide Prophet results from multiple search engines 2
InterProScan functional annotation 9
Intersect the intervals of two datasets Filtering 6
Intersect multiple VCF datasets 2
Intersect intervals find overlapping intervals in various ways 22
IQ-TREE Phylogenomic / evolutionary tree construction from multiple sequences 7
ISEScan Insertion Sequence Elements detection in prokaryotic genomes 1
isochore Plots isochores in large DNA sequences 5
ivar consensus Call consensus from aligned BAM file 9
ivar filtervariants Filter variants across replicates or multiple samples aligned using the same reference 7
ivar getmasked Detect primer mismatches and get primer indices for the amplicon to be masked 4
ivar removereads Remove reads from trimmed BAM file 11
ivar trim Trim reads in aligned BAM 13
ivar variants Call variants from aligned BAM file 9
IWTomics Load Smooth and Plot 1
IWTomics Plot with Threshold on Test Scale 1
IWTomics Test and Plot 1
jackhmmer iteratively search a protein sequence against a protein database (PSIBLAST-like) 8
JBrowse genome browser Map drawing Sequence visualisation 31
JBrowse - Data Directory to Standalone upgrades the bare data directory to a full JBrowse instance Conversion 30
jellyfish 1
Join the intervals of two datasets side-by-side Aggregation 5
Join two files 12
Join +/- Ions Join positive and negative ionization-mode W4M datasets for the same samples 1
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 4
Join two files on column allowing a small difference 2
JQ process JSON 1
Junction Annotation compares detected splice junctions to reference gene model 12
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 12
Kallisto pseudo - run pseudoalignment on RNA-Seq transcripts 6
Kallisto quant - quantify abundances of RNA-Seq transcripts 8
khmer: Abundance Distribution Calculate abundance distribution of k-mers using pre-made k-mer countgraphs 4
khmer: Abundance Distribution (all-in-one) Calculate abundance distribution of k-mers 4
khmer: Count Median Count the median/avg k-mer abundance for each sequence 4
khmer: Extract partitions Separate sequences that are annotated with partitions into grouped files 4
khmer: Filter reads by minimal k-mer abundance 4
khmer: Filter reads below k-mer abundance of 50 4
khmer: Normalize By Median Filter reads using digital normalization via k-mer abundances Sequence file editing Sequence word comparison 5
khmer: Sequence partition all-in-one Load, partition, and annotate sequences 4
Kraken assign taxonomic labels to sequencing reads 8
Kraken-filter filter classification by confidence score 4
Kraken-mpa-report view report of classification for multiple samples 5
Kraken-report view sample report of a classification 5
Kraken-translate convert taxonomy IDs to names 4
Kraken2 assign taxonomic labels to sequencing reads 5
Krona pie chart from taxonomic profile 10
LASTZ : align long sequences 7
Lastz paired reads map short paired reads against reference sequence 2
LASTZ_D : estimate substitution scores matrix 5
LAV to BED Converts a LAV formatted file to BED format 1
LCMS matching Annotation of LCMS peaks using matching on a in-house spectra database or on PeakForest spectra database. 3
LD linkage disequilibrium and tag SNPs 1
Lefse description 5
Length Distribution chart 2
Libshuff Cramer-von Mises tests communities for the same structure 5
limma Perform differential expression with limma-voom or limma-trend Differential gene expression profiling RNA-seq read count analysis 19
lindna Draws linear maps of DNA constructs 5
Line/Word/Character count of a dataset 1
Lineage Branch Analysis using StemID inspects branches of a lineage tree 6
Lineage computation using StemID generates lineage from prior clustering 6
LINKS - scaffold genome assemblies with long reads 1
List.otulabels Lists otu labels from shared or relabund file 5
List.seqs Lists the names (accnos) of the sequences 5
Lofreq filter called variants posteriorly 4
Machine Learning Visualization Extension includes several types of plotting for machine learning 6
MACS2 bdgbroadcall Call broad peaks from bedGraph output 9
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph 9
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files 10
MACS2 bdgpeakcall Call peaks from bedGraph output 9
MACS2 callpeak Call peaks from alignment results 12
MACS2 filterdup Remove duplicate reads at the same position 9
MACS2 predictd Predict 'd' or fragment size from alignment results 9
MACS2 randsample Randomly sample number or percentage of total reads 9
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) 9
MACS2.1.1 Model-based Analysis of ChIP-Seq: peak calling 2
MAF Coverage Stats Alignment coverage information 3
MAF to BED Converts a MAF formatted file to the BED format 1
MAF to FASTA Converts a MAF formatted file to FASTA format 1
MAF to Interval Converts a MAF formatted file to the Interval format 1
MAFFT Multiple alignment program for amino acid or nucleotide sequences 9
MAFFT add Align a sequence,alignment or fragments to an existing alignment. 6
MAGeCK count - collect sgRNA read counts from read mapping files 8
MAGeCK GSEA - a fast implementation of Gene Set Enrichment Analysis 4
MAGeCK mle - perform maximum-likelihood estimation of gene essentiality scores 5
MAGeCK pathway - given a ranked gene list, test whether one pathway is enriched 4
MAGeCKs test - given a table of read counts, perform the sgRNA and gene ranking 5
Make Design Assign groups to Sets 5
Make.biom Make biom files from a shared file 5
Make.contigs Aligns paired forward and reverse fastq files to contigs as fasta and quality 6
Make.fastq Convert fasta and quality to fastq 6
Make.group Make a group file 6
Make.lefse create a lefse formatted input file from mothur's output files 6
Make.lookup allows you to create custom lookup files for use with shhh.flows 5
Make.shared Make a shared file from a list and a group 5
Make.sra creates the necessary files for a NCBI submission 5
Maker genome annotation pipeline 10
MALDIquant peak detection Peak detection, binning and filtering for mass-spectrometry imaging data 7
MALDIquant preprocessing Preprocessing of mass-spectrometry imaging data 4
Manipulate AnnData object 10
Manipulate FASTQ reads on various attributes Sequence conversion 4
Mantel Mantel correlation coefficient between two matrices. 5
Map annotation ids on a Maker annotation 5
Map with Bowtie for Illumina 7
Map with BWA - map short reads (< 100 bp) against reference genome 12
Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 14
Map with minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences Sequence alignment 18
MapBed apply a function to a column for each overlapping interval 21
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 17
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 16
marscan Finds MAR/SAR sites in nucleic sequences 5
mash screen determines how well query sequences are contained within a pool of sequences 3
mash sketch Create a reduced representation of a sequence or set of sequences, based on min-hashes 1
maskfeat Mask off features of a sequence 5
MaskImage hide portions of an image based on previously identified objects 2
maskseq Mask off regions of a sequence 5
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
MaSuRCA simple The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit without config 1
matcher Finds the best local alignments between two sequences 5
Max SuCOS score - determine maximum SuCOS score of ligands against clustered fragment hits 7
MaxBin2 clusters metagenomic contigs into bins 4
MaxQuant Imputation Protein quantification Statistical calculation 17
MaxQuant (using mqpar.xml) Imputation Protein quantification Statistical calculation 9
MDTraj file converter - interconvert between MD trajectory file formats. 5
MeanQualityByCycle chart distribution of base qualities 14
MeasureGranularity output spectra of size measurements of the textures 2
MeasureImageAreaOccupied measure the area in an image occupied by objects 2
MeasureImageIntensity measure several intensity features across an entire image 2
MeasureImageQuality measure features that indicate image quality 2
MeasureObjectIntensity measure several intensity features for identified objects 2
MeasureObjectSizeShape measure area and shape features of identified objects 2
MeasureTexture quantify the roughness and smoothness of the textures 2
medaka consensus pipeline Assembly polishing via neural networks 11
medaka consensus tool Assembly polishing via neural networks 10
medaka variant tool decodes variant calls from medaka consensus output 14
MEGAHIT for metagenomics assembly 7
megamerger Merge two large overlapping nucleic acid sequences 5
Merge MetaPhlAn abundance tables Nucleic acid sequence analysis Phylogenetic analysis 8
Merge the overlapping intervals of a dataset Sequence merging 5
Merge multiple VCF datasets 2
Merge Columns together 4
Merge GROMACS topologies and GRO files 7
Merge.count Merge count tables 2
Merge.files Merge data 5
Merge.groups Merge groups in a shared file 5
Merge.sfffiles Merge SFF files 5
Merge.taxsummary Merge tax.summary files 6
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 14
merger Merge two overlapping nucleic acid sequences 5
MergeSamFiles merges multiple SAM/BAM datasets into one 14
Merqury evaluate the assembly quality Genome assembly 4
Meryl a genomic k-mer counter and sequence utility Genome assembly 8
MetaBAT2 metagenome binning 3
Metagenome Contributions of OTUs to user-specified functions 2
MetaPhlAn to profile the composition of microbial communities Nucleic acid sequence analysis Phylogenetic analysis 7
MetaPhlAn2 to profile the composition of microbial communities 2
metaplasmidSPAdes extract and assembly plasmids from metagenomic data 6
metaQuantome: create samples file by specifying the experiment's groups and associated column names 6
metaQuantome: database download the GO, EC, and NCBI databases 6
metaQuantome: expand a set of functional or taxonomy annotations 6
metaQuantome: filter for quality, redundancy, and sample coverage 6
metaQuantome: stat differential analysis of functional expression and taxonomic abundance 6
metaQuantome: visualize taxonomic analysis, functional analysis, and function-taxonomy analysis results 6
metaSPAdes metagenome assembler 12
Metastats generate principle components plot data 5
metaviralSPAdes extract and assembly viral genomes from metagenomic data 6
MetaWRAP metagenome binning pipeline 1
MethylDackel A tool for processing bisulfite sequencing alignments Gene methylation analysis 7
metilene calling differentially methylated regions from bisulfite sequencing data 5
Mimarks.attributes Reads bioSample Attributes xml and generates source for get.mimarkspackage command 5
MiModD Convert converts sequence data into different formats 2
MiModD Coverage Statistics calculates coverage statistics for a BCF file as generated by the MiModd Variant Calling tool 2
MiModD Deletion Calling (for PE data) predicts deletions in one or more aligned paired-end read samples based on coverage of the reference genome and on insert sizes 2
MiModD Extract Variant Sites from a BCF file 2
MiModD File Information provides summary reports for supported sequence data formats. 3
MiModD NacreousMap maps phenotypically selected variants by multi-variant linkage analysis 3
MiModD Read Alignment maps sequence reads to a reference genome using SNAP 1
MiModD Rebase Sites from a VCF file 3
MiModD Reheader takes a BAM file and generates a copy with the original header (if any) replaced or modified by that found in a template SAM file 2
MiModD Report Variants in a human-friendly format that simplifies data exploration 3
MiModD Run Annotation writes run metadata in SAM format for attaching it to sequenced reads data 2
MiModD Sort takes a SAM/BAM dataset and generates a coordinate/name-sorted copy 2
MiModD Variant Calling generates a BCF file of position-specific variant likelihoods and coverage information based on a reference sequence and reads aligned against it 2
MiModD VCF Filter extracts lines from a vcf variant file based on field-specific filters 3
Minia Short-read assembler based on a de Bruijn graph 3
miniasm Ultrafast de novo assembly for long noisy reads 7
miRcounts Counts miRNA alignments from small RNA sequence data 1
MiRDeep2 identification of novel and known miRNAs 3
MiRDeep2 Mapper process and map reads to a reference genome 3
MiRDeep2 Quantifier fast quantitation of reads mapping to known miRBase precursors 2
Mismatch Profile calculates the distribution of mismatches across reads 6
MITObim mitochondrial baiting and iterative mapping 1
MITOS2 de-novo annotation of metazoan mitochondrial genomes 3
MLST Scans genomes against PubMLST schemes 4
MLST List Lists available schemes for the MLST tool 4
MOB-Recon Type contigs and extract plasmid sequences 2
MOB-Typer Get the plasmid type and mobility given its sequence 2
Model Prediction predicts on new data using a preffited model 7
moFF extracts MS1 intensities from spectrum files 5
mol2-to-mol converter 2
Molecule to fingerprint conversion to several different fingerprint formats 5
Morpheus database search algorithm for high-resolution tandem mass spectra 2
mothur.ref.taxonomy-to-mothur.seq.taxonomy converter 2
msbar Mutate sequence beyond all recognition 5
msconvert Convert and/or filter mass spectrometry files 5
MSFraggerAdapter Peptide Identification with MSFragger.Important note:The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available for use on related service offerings supported by the University of Tubingen and the Center forIntegrative Bioinformatics. Per the license agreement the use of the pipeline and associated materials is for academic research, non-commercial or educational purposes. Any commercial use inquiries must be directed to the University of Michigan Technology Transfer Office at techtransfer@umich.edu. All right title and interest in MS Fragger shall remain with the University of Michigan.For details, please see the supplied license file or https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License.txt 4
MSGFPlusAdapter MS/MS database search using MS-GF+. 6
MSI classification spatial classification of mass spectrometry imaging data 10
MSI combine combine several mass spectrometry imaging datasets into one 11
MSI data exporter exports imzML and Analyze7.5 to tabular files 7
MSI filtering tool for filtering mass spectrometry imaging data 8
MSI mz images mass spectrometry imaging m/z heatmaps 8
MSI plot spectra mass spectrometry imaging mass spectra plots 10
MSI preprocessing mass spectrometry imaging preprocessing 11
MSI Qualitycontrol mass spectrometry imaging QC 11
MSI segmentation mass spectrometry imaging spatial clustering 8
MSnbase readMSData Imports mass-spectrometry data files 3
MSstats statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry 5
MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 4
Multi-Join (combine multiple files) 10
multiBamSummary calculates average read coverages for a list of two or more BAM/CRAM files 17
multiBigwigSummary calculates average scores for a list of two or more bigwig files 17
Multilevel Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package 1
MultiplexResolver Completes peptide multiplets and resolves conflicts within them. 4
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 18
Mummer Align two or more sequences Read mapping Sequence alignment 5
Mummerplot Generate 2-D dotplot of aligned sequences Read mapping Sequence alignment 5
MuSiC Deconvolution estimate cell type proportions in bulk RNA-seq data 4
mz to sqlite Extract mzIdentML and associated proteomics datasets into a SQLite DB 5
MzTabExporter Exports various XML formats to an mzTab file. 5
Naive Variant Caller (NVC) - tabulate variable sites from BAM datasets 5
NanoFilt Filtering and trimming of long read sequencing data 1
NanoPlot Plotting suite for Oxford Nanopore sequencing data and alignments 6
Nanopolish eventalign - Align nanopore events to reference k-mers 3
Nanopolish methylation - Classify nucleotides as methylated or not. 3
Nanopolish polyA - Estimate the length of the poly-A tail on direct RNA reads. 3
Nanopolish variants - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences 3
Natural Product likeness calculator - calculates the similarity of the molecule to the structure space covered by known natural products 3
NCBI Accession Download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 3
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 18
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 18
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 15
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 18
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 16
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 18
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 14
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 15
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI get species taxids 2
Nearest Neighbors Classification 11
needle Needleman-Wunsch global alignment 5
neostore.zip-to-neostore converter 1
NetCDF xarray Metadata Info summarize content of a Netcdf file 5
NetCDF xarray Selection extracts variable values with custom conditions on dimensions 5
newcpgreport Report CpG rich areas 5
newcpgseek Reports CpG rich region 5
Newick Display visualize a phylogenetic tree Phylogenetic tree visualisation 2
newseq Type in a short new sequence 5
Nextclade Viral genome clade assignment, mutation calling, and sequence quality checks 18
NGSfilter Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers 3
nhmmer search a DNA model or alignment against a DNA database (BLASTN-like) 8
nhmmscan search DNA sequence(s) against a DNA profile database 8
Nmds generate non-metric multidimensional scaling data 6
NMR spectra alignment based on the Cluster-based Peak Alignment (CluPA) algorithm 2
NMR_Bucketing Bucketing and integration of NMR Bruker raw data 4
NMR_Preprocessing Preprocessing of 1D NMR spectra 4
NMR_Read Read Bruker NMR raw files 3
noreturn Removes carriage return from ASCII files 5
Normalization Normalization of (preprocessed) spectra 4
Normalize the relative abundance of each OTU by the predicted number of 16S copies 2
Normalize with scanpy 7
Normalize.shared Normalize the number of sequences per group to a specified level 5
NormalizeFasta normalize fasta datasets 14
notseq Exclude a set of sequences and write out the remaining ones 5
NOVOplasty de novo assembler for short circular genomes 3
nthseq Writes one sequence from a multiple set of sequences 5
NucBed profile the nucleotide content of intervals in a FASTA file 21
Nucleotide Variants Identifies nucleotide variants 2
Nucmer Align two or more sequences Read mapping Sequence alignment 5
Numeric Clustering 12
NxN clustering of molecular fingerprints 5
obiannotate Adds/Edits sequence record annotations 3
obiclean tags a set of sequences for PCR/sequencing errors identification 3
obiconvert converts sequence files to different output formats 3
obigrep Filters sequence file 3
obisort sorts sequence records according to the value of a given attribute 3
obistat computes basic statistics for attribute values 3
obitab converts sequence file to a tabular file 3
obiuniq 3
octanol Displays protein hydropathy 5
oddcomp Find protein sequence regions with a biased composition 5
Online data fetching ... 2
OpenSwathAnalyzer Picks peaks and finds features in an SWATH-MS or SRM experiment. 4
OpenSwathAssayGenerator Generates assays according to different models for a specific TraML 4
OpenSwathConfidenceScoring Compute confidence scores for OpenSwath results 5
OpenSwathDecoyGenerator Generates decoys according to different models for a specific TraML 5
OpenSwathDIAPreScoring Scoring spectra using the DIA scores. 4
OpenSwathFileSplitter Splits SWATH files into n files, each containing one window. 5
OpenSwathMzMLFileCacher This tool caches the spectra and chromatogram data of an mzML to disk. 4
OpenSwathRTNormalizer This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. 5
OpenSwathWorkflow Complete workflow to run OpenSWATH 4
OPLS-DA_Contrasts OPLS-DA Contrasts of Univariate Results 5
Otu.association Calculate the correlation coefficient for the otus 5
Otu.hierarchy Relate OTUs at different distances 5
OTUTable Convert UCLUST format from Vsearch to OTU Table 1
OverlayOutlines places outlines of objects over a desired image. 2
Paired-end histogram of insert size frequency 1
Pairwise.seqs calculate uncorrected pairwise distances between sequences 5
palindrome Looks for inverted repeats in a nucleotide sequence 5
Pangolin Phylogenetic Assignment of Outbreak Lineages 22
Parallel Coordinates Plot of tabular data 3
parquet-to-csv converter 1
Parse mitochondrial blast overlap-conscious coverage calculation between scaffold-accession number pairs from blast output 2
Parse.list Generate a List file for each group 5
Parsimony Describes whether two or more communities have the same structure 5
Partition genes into expression clusters after differential expression analysis using a Trinity assembly 12
Paste two files side by side 1
pasteseq Insert one sequence into another 5
Pathview for pathway based data integration and visualization 3
patmatdb Search a protein sequence with a motif 5
PCA - principal component analysis using Bio3D 2
Pca Principal Coordinate Analysis for a shared file 6
PCA visualization - generate trajectories of principal components of atomic motion 2
Pcoa Principal Coordinate Analysis for a distance matrix 5
Pcr.seqs Trim sequences 6
pdb-to-gro converter 1
PeakPickerHiRes Finds mass spectrometric peaks in profile mass spectra. 4
Pear Paired-End read merger 5
PEAR Statistics Generate paired-end reads overlap Statistic from PEAR log file 1
pepcoil Predicts coiled coil regions 5
pepinfo Plots simple amino acid properties in parallel 5
pepnet Displays proteins as a helical net 5
PepPointer classify genomic location of peptides 2
pepstats Protein statistics 5
Peptide Genomic Coordinate Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB 2
Peptide Prophet Calculate Peptide Prophet statistics on search results 2
Peptide Shaker Perform protein identification using various search engines based on results from SearchGUI 19
PeptideIndexer Refreshes the protein references for all peptide hits. 6
pepwheel Shows protein sequences as helices 5
pepwindow Displays protein hydropathy 5
pepwindowall Displays protein hydropathy of a set of sequences 5
PepXML to Table Converts a pepXML file to a tab delimited text file 1
Percolator accurate peptide identification 2
phmmer search a protein sequence against a protein database (BLASTP-like) 8
Phylo.diversity Alpha Diversity calculates unique branch length 5
Phyloseq Abundance plot Phyloseq Abundance Plot with the factors of choice 1
Phyloseq Abundance Taxonomy Phyloseq Abundance Plot on Taxonomy level 1
Phyloseq Biom Filtering biom file filter 1
Phyloseq DESeq2 Perform differential expression analysis of BIOM file 1
Phyloseq Network Plot Phyloseq Network Plot 1
Phyloseq Ordination Plot ordination plotting 1
Phyloseq Richness Phyloseq Richness Plot 1
Phylotype Assign sequences to OTUs based on taxonomy 5
PhyML Phylogeny software based on the maximum-likelihood method. Phylogenetic analysis Phylogenetic inference (from molecular sequences) 4
Phyogenetic reconstruction with RAxML - Maximum Likelihood based inference of large phylogenetic trees 6
Picard Collect Sequencing Artifact Metrics Collect metrics to quantify single-base sequencing artifacts 6
Pileup-to-Interval condenses pileup format into ranges of bases 4
pilon An automated genome assembly improvement and variant detection tool 2
PIPE-T A tool for analyzing RTqPCR expression data 1
Pipeline Builder an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers 11
plasmidSPAdes extract and assembly plasmids from WGS data 6
Plot with scanpy 8
Plot actual vs predicted curves and residual plots of tabular data 1
Plot confusion matrix, precision, recall and ROC and AUC curves of tabular data 2
Plot performance per cell in nanopore reads 2
Plot signals for nanopore reads 2
plotcon Plot quality of conservation of a sequence alignment 5
plotCorrelation Create a heatmap or scatterplot of correlation scores between different samples 16
plotCoverage assesses the sequencing depth of BAM/CRAM files 16
plotDEXSeq Visualization of the per gene DEXSeq results 5
plotEnrichment plots read/fragment coverage over sets of regions 12
plotFingerprint plots profiles of BAM files; useful for assesing ChIP signal strength 17
plotHeatmap creates a heatmap for score distributions across genomic regions 17
plotorf Plot potential open reading frames 5
plotPCA Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output 16
plotProfile creates a profile plot for score distributions across genomic regions 16
Plotting tool for multiple series and graph types 5
PMIDs to PubTator binary matrix 1
Poisson two-sample test 1
polydot Displays all-against-all dotplots of a set of sequences 5
Porechop adapter trimmer for Oxford Nanopore reads 3
Pout2mzid add Percolator scoring to mzIdentML 2
Pre.cluster Remove sequences due to pyrosequencing errors 5
Predict Metagenome based on the abundance of OTUs and a functional database 2
preg Regular expression search of a protein sequence 6
Prepare receptor Tool to prepare receptor for docking with Autodock Vina 2
Pretext Snapshot 2
PretextMap converts SAM or BAM files into genome contact maps 7
prettyplot Displays aligned sequences, with colouring and boxing 5
prettyseq Output sequence with translated ranges 5
Primer.design identify sequence fragments that are specific to particular OTUs 5
primersearch Searches DNA sequences for matches with primer pairs 5
proFIA Preprocessing of FIA-HRMS data 2
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 11
proportional venn from 2-3 sets 1
Protein Database Downloader 6
Protein Prophet Calculate Protein Prophet statistics on search results 2
ProteinQuantifier Compute peptide and protein abundances 4
ProtXML to Table Converts a ProtXML file to a table 1
PubChem Assay Downloader as canonical SMILES 3
PubChem Download as canonical SMILES 3
PubMed query download a defined number of abstracts or PMIDs from PubMed 1
Purge overlaps and haplotigs in an assembly based on read depth (purge_dups) 6
Pycoqc 1
pyGenomeTracks plot genomic data tracks 12
PyProphet merge Merge multiple osw files 1
PyProphet peptide Peptide error-rate estimation 1
PyProphet protein Protein error-rate estimation 1
PyProphet score Error-rate estimation for MS1, MS2 and transition-level data 3
QualiMap BamQC 5
QualiMap Multi-Sample BamQC 2
QualiMap RNA-Seq QC 3
Quality control Performs quality control on FASTQ reads. 2
Quality format converter (ASCII-Numeric) 3
Quality Metrics Metrics and graphics to check the quality of the data 2
QualityScoreDistribution chart quality score distribution 14
Quasispecies Distance Calculate the evolutionary distance between viral quasispecies. 2
Quast Genome assembly Quality 14
Query Tabular using sqlite sql 8
Racon Consensus module for raw de novo DNA assembly of long uncorrected reads 8
Rarefaction.shared Generate inter-sample rarefaction curves for OTUs 5
Rarefaction.single Generate intra-sample rarefaction curves for OTUs 6
Raven De novo assembly of Oxford Nanopore Technologies data 5
Raw Tools Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files. 1
Read Distribution calculates how mapped reads were distributed over genome feature 12
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 10
Read GC determines GC% and read count 10
Read length statistics from a set of FAST5 files 2
Read NVC to check the nucleotide composition bias 10
Read Quality determines Phred quality score 10
Realign reads with LoFreq viterbi 5
Rebase GFF3 features against parent features 2
Regex Find And Replace 5
Regroup a HUMAnN2 generated table by features 4
Regroup HUMAnN table features Nucleic acid sequence analysis Phylogenetic analysis 2
reheader Rename sequence header in FASTQ file 1
Reheader copy SAM/BAM header between datasets 4
RelateObjects assign relationships parent-children between objects 2
Remove beginning of a file 1
Remove confounders with scanpy 7
Remove sequencing artifacts 5
Remove.dists Removes distances from a phylip or column file 6
Remove.groups Remove groups from groups,fasta,names,list,taxonomy 5
Remove.lineage Picks by taxon 5
Remove.otulabels Removes OTU labels 6
Remove.otus Removes OTUs from various file formats 5
Remove.rare Remove rare OTUs 5
Remove.seqs Remove sequences by name 6
Rename features of a HUMAnN generated table Nucleic acid sequence analysis Phylogenetic analysis 2
Rename sequences 5
Rename.seqs Rename sequences by concatenating the group name 2
Renormalize a HUMAnN2 generated table 5
Renormalize a HUMAnN generated table Nucleic acid sequence analysis Phylogenetic analysis 3
ReorderSam reorder reads to match ordering in reference sequences 17
RepeatMasker screen DNA sequences for interspersed repeats and low complexity regions Repeat sequence analysis 8
RepeatModeler Model repetitive DNA 2
RepEnrich Repeat Element Profiling 1
Replace parts of text 12
Replace column by values which are defined in a convert file 2
Replace Text in a specific column 11
Replace Text in entire line 11
ReplaceSamHeader replace header in a SAM/BAM dataset 17
Reverse columns in a tabular file 5
Reverse Complement a MAF file 1
Reverse-Complement 5
Reverse.seqs Reverse complement the sequences 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 14
RevertSam revert SAM/BAM datasets to a previous state 14
revseq Reverse and complement a sequence 5
RmDup remove PCR duplicates 5
RMSD Analysis using Bio3D 2
RMSF Analysis using Bio3D 2
RNA fragment size calculates the fragment size for each gene/transcript 8
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly Sequence alignment 19
RNA STARSolo mapping, demultiplexing and gene quantification for single cell RNA-seq Sequence alignment 8
RNA/DNA converter 5
RnaChipIntegrator Integrated analysis of 'gene' and 'peak' data 3
RNASeq samples quality check for transcript quantification 11
rnaSPAdes de novo transcriptome assembler 13
rnaviralSPAdes de novo assembler for transcriptomes, metatranscriptomes and metaviromes 6
Roary the pangenome pipeline - Quickly generate a core gene alignment from gff3 files 8
Row Means Calculates the mean of a row of numbers for an entire table 1
RPKM Saturation calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 12
rxDock cavity definition - generate the active site definition needed for rxDock docking 3
rxDock docking - perform protein-ligand docking with rxDock 4
Sailfish transcript quantification from RNA-seq data 4
Salmon quant Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads 13
salmonKallistoMtxTo10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data 3
SALSA scaffold long read assemblies with Hi-C 5
SAM-to-BAM convert SAM to BAM 8
sam-to-bam converter 1
sam-to-bigwig converter 1
sam-to-qname_sorted.bam converter 1
sam-to-unsorted.bam converter 1
SampComp to compare Nanopolished datasets 2
Sample, Slice or Filter BAM on flags, fields, and tags using Sambamba 1
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 19
Samtools calmd recalculate MD/NM tags 4
Samtools fastx extract FASTA or FASTQ from alignment files 3
Samtools flagstat tabulate descriptive stats for BAM datset 8
Samtools merge merge multiple sorted alignment files 3
samtools mpileup multi-way pileup of variants 11
Samtools sort order of storing aligned sequences 7
Samtools split BAM dataset on readgroups 5
Samtools stats generate statistics for BAM dataset 7
Samtools view - reformat, filter, or subsample SAM, BAM or CRAM 9
SaveImages or movie files 2
Scanpy BBKNN batch-balanced K-nearest neighbours 6
Scanpy ComBat adjust expression for variables that might introduce batch effect 6
Scanpy ComputeGraph to derive kNN graph 16
Scanpy DiffusionMap calculate diffusion components 11
Scanpy DPT diffusion pseudotime inference 11
Scanpy FilterCells based on counts and numbers of genes expressed 15
Scanpy FilterGenes based on counts and numbers of cells expressed 15
Scanpy FindCluster based on community detection on KNN graph 17
Scanpy FindMarkers to find differentially expressed genes between groups 17
Scanpy FindVariableGenes based on normalised dispersion of expression 13
Scanpy Harmony adjust principal components for variables that might introduce batch effect 7
Scanpy MNN correct batch effects by matching mutual nearest neighbors 6
Scanpy NormaliseData to make all cells having the same total expression 14
Scanpy PAGA trajectory inference 10
Scanpy ParameterIterator produce an iteration over a defined parameter 5
Scanpy Plot Scrublet visualise multiplet scoring distribution 2
Scanpy PlotEmbed visualise cell embeddings 12
Scanpy PlotTrajectory visualise cell trajectories 11
Scanpy Read10x into hdf5 object handled by scanpy 13
Scanpy RegressOut variables that might introduce batch effect 10
Scanpy RunFDG visualise cell clusters using force-directed graph 11
Scanpy RunPCA for dimensionality reduction 14
Scanpy RunTSNE visualise cell clusters using tSNE 15
Scanpy RunUMAP visualise cell clusters using UMAP 14
Scanpy ScaleData to make expression variance the same for all genes 13
Scanpy Scrublet remove multiplets from annData objects with Scrublet 2
Scater: Calculate QC metrics Computes QC metrics from single-cell expression matrix 4
Scater: filter SCE with user-defined parameters or PCA 5
Scater: PCA plot cell-level reduced dimension of a normalised SCE 4
Scater: plot library QC to visualise library size, feature counts and mito gene expression 4
Scatterplot with ggplot2 10
Screen.seqs Screen sequences 6
SDF to Fingerprint - extract fingerprints from sdf file metadata 5
Search ChEMBL database for compounds which are similar to a SMILES string 6
Search engine output to Pin converter to create Percolator input files 2
Search GUI Perform protein identification using various search engines and prepare results for input to Peptide Shaker 22
Search in textfiles (grep) 11
SearchToLib Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data 3
Secure Hash / Message Digest on a dataset 2
Select lines that match an expression Filtering 3
Select first lines from a dataset Filtering 4
Select first lines from a dataset (head) 9
Select last lines from a dataset 2
Select last lines from a dataset (tail) 9
Select random lines from a file 2
Select sequences by ID from a tabular file 3
Send to cloud 1
Sens.spec Determine the quality of OTU assignment 6
Seq.error assess error rates in sequencing data 5
seqmatchall All-against-all comparison of a set of sequences 5
seqret Reads and writes sequences 5
seqtk_comp get the nucleotide composition of FASTA/Q 6
seqtk_cutN cut sequence at long N 6
seqtk_dropse drop unpaired from interleaved Paired End FASTA/Q 6
seqtk_fqchk fastq QC (base/quality summary) 6
seqtk_hety regional heterozygosity 6
seqtk_listhet extract the position of each het 6
seqtk_mergefa merge two FASTA/Q files 6
seqtk_mergepe interleave two unpaired FASTA/Q files for a paired-end file 6
seqtk_mutfa point mutate FASTA at specified positions 6
seqtk_randbase choose a random base from hets 6
seqtk_sample random subsample of fasta or fastq sequences 6
seqtk_seq common transformation of FASTA/Q 6
seqtk_subseq extract subsequences from FASTA/Q files 6
seqtk_trimfq trim FASTQ using the Phred algorithm 6
Sequence Logo generator for fasta (eg Clustal alignments) 2
Seurat - toolkit for exploration of single-cell RNA-seq data 12
SFF converter 1
Sffinfo Summarize the quality of sequences 5
Shasta De novo assembly of long read sequencing data 1
Shhh.flows Denoise flowgrams (PyroNoise algorithm) 5
Shhh.seqs Denoise program (Quince SeqNoise) 5
Shovill Faster SPAdes assembly of Illumina reads 8
Show nucleotide distribution in nanopore sequencing reads 2
Show quality score distribution in nanopore sequencing reads 2
Show-Coords Parse delta file and report coordinates and other information Read mapping Sequence alignment 5
showfeat Show features of a sequence 5
shuffleseq Shuffles a set of sequences maintaining composition 5
SICER Statistical approach for the Identification of ChIP-Enriched Regions 3
sigcleave Reports protein signal cleavage sites 5
sirna Finds siRNA duplexes in mRNA 5
sistr_cmd Salmonella In Silico Typing Resource commandline tool for serovar prediction 3
sixpack Display a DNA sequence with 6-frame translation and ORFs 7
skipseq Reads and writes sequences, skipping first few 5
Slice BAM by genomic regions 5
Slice MD trajectories using the MDTraj package 3
smi-to-mol converter 2
smi-to-smi converter 2
Smudgeplot inference of ploidy and heterozygosity structure using whole genome sequencing 1
sniffles Structural variation caller using third generation sequencing 1
snippy Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 11
snippy-clean_full_aln Replace any non-standard sequence characters in snippy 'core.full.aln' file. 4
snippy-core Combine multiple Snippy outputs into a core SNP alignment 10
SNP distance matrix Compute distance in SNPs between all sequences in a FASTA file 2
SNP splitter splits multicharacter entries into separate lines 1
SNP table merger merges any number of SNP tables into one 1
SnpEff build: database from Genbank or GFF record 13
SnpEff chromosome-info: list chromosome names/lengths 8
SnpEff databases: list available databases 13
SnpEff download: download a pre-built database 13
SnpEff eff: annotate variants 11
SnpEff eff: annotate variants for SARS-CoV-2 1
snpFreq significant SNPs in case-control data 2
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift Extract Fields from a VCF file into a tabular file 7
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 9
SnpSift rmInfo remove INFO field annotations 8
SnpSift Variant Type Annotate with variant type 8
SnpSift vcfCheck basic checks for VCF specification compliance 8
Sort data in ascending or descending order Sorting 3
Sort data in ascending or descending order 11
Sort a row according to their columns 12
Sort assembly 5
Sort.seqs put sequences in different files in the same order 6
SortSam sort SAM/BAM dataset 14
SPAdes genome assembler for genomes of regular and single-cell projects Genome assembly 16
Split a HUMAnN table into 2 tables (one stratified and one unstratified) Nucleic acid sequence analysis Phylogenetic analysis 3
Split file to dataset collection 7
Split MAF blocks by Species 1
Split.abund Separate sequences into rare and abundant groups 5
Split.groups Generates a fasta file for each group 5
splitter Split a sequence into (overlapping) smaller sequences 5
SQLite to tabular for SQL query 3
Stacks2: clone filter Identify PCR clones 8
Stacks2: cstacks Generate catalog of loci 8
Stacks2: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 8
Stacks2: gstacks Call variants, genotypes and haplotype 8
Stacks2: kmer filter Identify PCR clones 8
Stacks2: populations Calculate population-level summary statistics 8
Stacks2: process radtags the Stacks demultiplexing script 8
Stacks2: process shortreads fast cleaning of randomly sheared genomic or transcriptomic data 8
Stacks2: reference map the Stacks pipeline with a reference genome (ref_map.pl) 8
Stacks2: sstacks Match samples to the catalog 8
Stacks2: tsv2bam Sort reads by RAD locus 8
Stacks2: ustacks Identify unique stacks 8
Stacks: assemble read pairs by locus run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers 6
Stacks: clone filter Identify PCR clones 2
Stacks: cstacks build a catalogue of loci 5
Stacks: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 5
Stacks: genotypes analyse haplotypes or genotypes in a genetic cross ('genotypes' program) 5
Stacks: populations analyze a population of individual samples ('populations' program) 5
Stacks: process radtags the Stacks demultiplexing script 5
Stacks: pstacks find stacks from short reads mapped to a reference genome 5
Stacks: reference map the Stacks pipeline with a reference genome (ref_map.pl) 5
Stacks: rxstacks make corrections to genotype and haplotype calls 5
Stacks: sstacks match stacks to a catalog 4
Stacks: statistics on stacks found for multiple samples 2
Stacks: ustacks align short reads into stacks 5
staramr Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes. 11
Starting Modules load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups) 2
Stitch Gene blocks given a set of coding exon intervals 4
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 17
StringTie merge transcripts 11
Sub.sample Create a sub sample 5
Subtract the intervals of two datasets Filtering 6
Subtract Whole Dataset from another dataset 2
Summary Statistics for any numerical column 3
Summary.qual Summarize the quality scores 6
Summary.seqs Summarize the quality of sequences 5
Summary.shared Summary of calculator values for OTUs 5
Summary.single Summary of calculator values for OTUs 6
Summary.tax Assign sequences to taxonomy 5
supermatcher Match large sequences against one or more other sequences 5
Support vector machines (SVMs) for classification 12
syco Synonymous codon usage Gribskov statistic plot 5
Symmetric Plot Symmetric Plot 1
T Test for Two Samples 2
Table Compute computes operations on table data 4
Table Merge Merging dataMatrix with a metadata table 2
Table to GFF3 2
Tabular to FASTQ converter Conversion 5
tabular-to-csv converter 1
Tabular-to-FASTA converts tabular file to FASTA format 2
tac reverse a file (reverse cat) 9
Tandem to pepXML Converts a tandem result file to pepXML 1
tar-to-directory converter 2
TargetedFileConverter Converts different transition files for targeted proteomics / metabolomics analysis. 4
TargetFinder plant small RNA target prediction tool Sequence alignment 2
Taxonomy-to-Krona convert a mothur taxonomy file to Krona input format 2
Taylor-Butina clustering of molecular fingerprints 5
TB Variant Filter M. tuberculosis H37Rv VCF filter 4
TB Variant Report - generate HTML report from SnpEff annotated M.tb VCF(s) 3
TB-Profiler Profile Infer strain types and drug resistance markers from sequences 15
tcode Fickett TESTCODE statistic to identify protein-coding DNA 5
Text reformatting with awk 13
Text transformation with sed 11
TextExporter Exports various XML formats to a text file. 4
textsearch Search sequence documentation. Slow, use SRS and Entrez! 5
Thermo RAW file converter 9
Tile tiles images together to form large montage images 2
tmap Displays membrane spanning regions 5
To categorical Converts a class vector (integers) to binary class matrix 2
TopHat Gapped-read mapper for RNA-seq data 9
Tophat Fusion Post post-processing to identify fusion genes 2
TrackObjects tracking objects throughout sequential frames of a series of images 2
Train Augustus ab-initio gene predictor 5
Train SNAP ab-initio gene predictor 1
TRAMS Tool for Rapid Annotation of Microbial SNPs 1
tranalign Align nucleic coding regions given the aligned proteins 5
Transcript Integrity Number evaluates RNA integrity at a transcript level 8
TransDecoder finds coding regions within transcripts 7
transeq Translate nucleic acid sequences 5
Translate BED transcripts cDNA in 3frames or CDS 1
Transpose rows/columns in a tabular file 5
Tree.shared Generate a newick tree for dissimilarity among groups 5
Trim leading or trailing characters 2
Trim Galore! Quality and adapter trimmer of reads 9
Trim sequences 5
Trim.flows partition by barcode, trim to length, cull by length and mismatches 5
Trim.seqs Trim sequences - primers, barcodes, quality 5
trimest Trim poly-A tails off EST sequences 5
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 15
trimseq Trim ambiguous bits off the ends of sequences 5
Trinity de novo assembly of RNA-Seq data 14
Trinotate functional transcript annotation 4
tRNA and tmRNA prediction (Aragorn) 3
tRNA prediction (tRNAscan) 2
Trycycler cluster cluster the contigs of your input assemblies into per-replicon groups Genome assembly 4
Trycycler consensus generate a consensus contig sequence for each cluster Genome assembly 4
Trycycler partition assign the reads to the clusters Genome assembly 4
Trycycler reconcile/msa reconcile the contigs within each cluster and perform a multiple sequence alignment Genome assembly 4
Trycycler subsample make a maximally-independent read subsets of an appropiate depth for your genome Genome assembly 4
twofeat Finds neighbouring pairs of features in sequences 5
UMI-tools count performs quantification of UMIs from BAM files 9
UMI-tools deduplicate Extract UMI from fastq files 6
UMI-tools extract Extract UMI from fastq files 12
Unfold columns from a table 11
unifrac.unweighted Describes whether two or more communities have the same structure 5
unifrac.weighted Describes whether two or more communities have the same structure 5
union Reads sequence fragments and builds one sequence 5
Unipept retrieve taxonomy for peptides 6
UniProt ID mapping and retrieval 4
UniProt download proteome as XML or fasta 6
Unique occurrences of each record 9
Unique lines assuming sorted input file 11
Unique.seqs Return unique sequences 5
Univariate Univariate statistics 2
Unpack pathway abundances to show the genes for each Nucleic acid sequence analysis Phylogenetic analysis 3
Unpack pathway abundances to show genes included 3
unsorted.bam-to-bigwig converter 1
Unzip Unzip file 1
ValidateSamFile assess validity of SAM/BAM dataset 15
Variant Frequency Plot Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data Aggregation 4
VarScan for variant detection 2
VarScan somatic Call germline/somatic and LOH variants from tumor-normal sample pairs 9
VCF to MAF Custom Track for display at UCSC 2
VCF-BEDintersect: Intersect VCF and BED datasets 5
vcf-to-bgzip converter 2
vcf-to-bigwig converter 1
vcf-to-tabix converter 2
VCF-VCFintersect: Intersect two VCF datasets 5
vcf_bgzip-to-tabix converter 2
VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset 5
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 5
VCFannotate: Intersect VCF records with BED annotations 5
VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset 5
VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 5
VCFcheck: Verify that the reference allele matches the reference genome 5
VCFcombine: Combine multiple VCF datasets 6
VCFcommonSamples: Output records belonging to samples common between two datasets 5
VCFdistance: Calculate distance to the nearest variant 5
VCFfilter: filter VCF data in a variety of attributes 8
VCFfixup: Count the allele frequencies across alleles present in each record in the VCF file 5
VCFflatten: Removes multi-allelic sites by picking the most common alternate 5
VCFgenotype-to-haplotype: Convert genotype-based phased alleles into haplotype alleles 5
VCFgenotypes: Convert numerical representation of genotypes to allelic 5
VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio 5
VCFleftAlign: Left-align indels and complex variants in VCF dataset 5
VCFprimers: Extract flanking sequences for each VCF record 5
VCFrandomSample: Randomly sample sites from VCF dataset 5
VCFselectsamples: Select samples from a VCF dataset 5
VCFsort: Sort VCF dataset by coordinate 6
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 6
vectorstrip Strips out DNA between a pair of vector sequences 5
velvetg Velvet sequence assembler for very short reads De-novo assembly Formatting 6
velveth Prepare a dataset for the Velvet velvetg Assembler De-novo assembly Formatting 6
VelvetOptimiser Automatically optimize Velvet assemblies 5
Venn Generate Venn diagrams for groups 5
VINA Docking tool to perform protein-ligand docking with Autodock Vina 5
Visualisation of compounds 5
Visualize the optimal scoring subnetwork 2
Visualize with Krona Visualise any hierarchical data 1
Volcano Plot create a volcano plot Visualisation 5
VSearch alignment Chimera detection Sequence clustering Sequence masking 6
VSearch chimera detection Chimera detection Sequence clustering Sequence masking 6
VSearch clustering Chimera detection Sequence clustering Sequence masking 7
VSearch dereplication Chimera detection Sequence clustering Sequence masking 7
VSearch masking Chimera detection Sequence clustering Sequence masking 6
VSearch search Chimera detection Sequence clustering Sequence masking 6
VSearch shuffling Chimera detection Sequence clustering Sequence masking 6
VSearch sorting Chimera detection Sequence clustering Sequence masking 7
W4m Data Subset Filter W4m data by values or metadata 9
Walnut PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data 3
water Smith-Waterman local alignment 5
Wavelet variance using Discrete Wavelet Transfoms 3
wig-to-bigwig converter 1
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2
wobble Wobble base plot 5
wordcount Counts words of a specified size in a DNA sequence 5
wordmatch Finds all exact matches of a given size between 2 sequences 5
X!Tandem MSMS Search Run an X!Tandem Search 2
xcms adjustRtime (retcor) Retention Time Correction 7
xcms fillChromPeaks (fillPeaks) Integrate areas of missing peaks 7
xcms findChromPeaks (xcmsSet) Chromatographic peak detection 8
xcms findChromPeaks Merger Merge xcms findChromPeaks RData into a unique file to be used by group 5
xcms get a sampleMetadata file which need to be filled with extra information 3
xcms groupChromPeaks (group) Perform the correspondence, the grouping of chromatographic peaks within and between samples. 8
xcms plot chromatogram Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) 5
xcms process history Create a summary of XCMS analysis 8
XMLValidator Validates XML files against an XSD schema. 4
XTandemAdapter Annotates MS/MS spectra using X! Tandem. 5
xtc-to-dcd converter 1
YAHS yet another HI-C scaffolding tool 4