1028 tool(s) found

Tool Description Topics Available version(s)
ABRicate Mass screening of contigs for antimicrobial and virulence genes Antimicrobial resistance prediction 6
ABRicate List List all of abricate's available databases. 6
Add column to an existing dataset 3
Add metadata to a BIOM table Conversion Format validation 3
AddCommentsToBam add comments to BAM dataset 12
AddOrReplaceReadGroups add or replaces read group information 12
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 6
Amova Analysis of molecular variance 6
Analyse canonical genes against 'peak' data using RnaChipIntegrator 3
Annotate a VCF dataset with custom filters 1
Annotate a VCF file (dbSNP, hapmap) 1
AnnotateBed annotate coverage of features from multiple files 17
annotateMyIDs annotate a generic set of identifiers 5
Anosim Non-parametric multivariate analysis of changes in community structure 6
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 4
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 5
BAM filter Removes reads from a BAM file based on criteria 4
BAM to BED converter 19
BAM to fastq Convert BAM file to fastq 1
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 7
BAM-to-SAM convert BAM to SAM 7
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 7
bamCompare normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them 16
bamCoverage generates a coverage bigWig file from a given BAM file 17
BamLeftAlign indels in BAM datasets 8
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 16
banana Bending and curvature plot in B-DNA 4
Bandage Image visualize de novo assembly graphs 4
Bandage Info determine statistics of de novo assembly graphs 4
Bar chart for multiple columns 1
Barcode Splitter 4
barrnap Locate ribosomal RNA's in a fasta file. (GFF output) 2
Base Coverage of all intervals Quantification 5
Batch_correction Corrects intensities for signal drift and batch-effects 7
bcftools annotate Annotate and edit VCF/BCF files 5
bcftools call SNP/indel variant calling from VCF/BCF 9
bcftools cnv Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values 6
bcftools concat Concatenate or combine VCF/BCF files 6
bcftools consensus Create consensus sequence by applying VCF variants to a reference fasta file 7
bcftools convert from vcf Converts VCF/BCF to IMPUTE2/SHAPEIT formats 5
bcftools convert to vcf Converts other formats to VCF/BCFk 5
bcftools counts plugin counts number of samples, SNPs, INDELs, MNPs and total sites 5
bcftools csq Haplotype aware consequence predictor 6
bcftools dosage plugin genotype dosage 5
bcftools fill-AN-AC plugin Fill INFO fields AN and AC 5
bcftools fill-tags plugin Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi 5
bcftools filter Apply fixed-threshold filters 5
bcftools fixploidy plugin Fix ploidy 5
bcftools gtcheck Check sample identity 5
bcftools impute-info plugin Add imputation information metrics to the INFO field 5
bcftools isec Create intersections, unions and complements of VCF files 5
bcftools List Samples in VCF/BCF file 5
bcftools mendelian plugin Count Mendelian consistent / inconsistent genotypes 5
bcftools merge Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file 5
bcftools missing2ref plugin Set missing genotypes 5
bcftools mpileup Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files 6
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 7
bcftools query Extracts fields from VCF/BCF file and prints them in user-defined format 5
bcftools reheader Modify header of VCF/BCF files, change sample names 5
bcftools roh HMM model for detecting runs of homo/autozygosity 5
bcftools setGT plugin Sets genotypes 5
bcftools stats Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats 5
bcftools tag2tag plugin Convert between similar tags, such as GL and GP 5
bcftools view Converts BCF format to VCF format 11
BED to BAM converter 17
BED to IGV create batch script for taking IGV screenshots 10
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED-to-GFF converter 2
BED12 to BED6 converter 16
BedCov calculate read depth for a set of genomic intervals 4
BEDPE to BAM converter 17
BedToIntervalList convert coordinate data into picard interval list format 12
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
Bin.seqs Order Sequences by OTU 6
Biom.info create shared and taxonomy files from biom 3
biosed Replace or delete sequence sections 4
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
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 2
btwisted Calculates the twisting in a B-DNA sequence 4
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 12
Bundle Collection Download a collection of files 1
Busco assess genome assembly and annotation completeness 6
cai CAI codon adaptation index 4
cai custom CAI codon adaptation index using custom codon usage file 4
Call and phase heterozygous SNPs 5
Call variants with LoFreq 3
CalMD recalculate MD/NM tags 5
CAMERA.annotate CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 11
CAMERA.combinexsAnnos Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations. 12
Canu assembler Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore 2
Categorize by collapsing hierarchical data to a specified functional level 3
Categorize Elements satisfying criteria 1
Change Case of selected columns 1
chaos Create a chaos game representation plot for a sequence 4
charge Protein charge plot 4
Check Format Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files 4
checktrans Reports STOP codons and ORF statistics of a protein 4
Chimera.bellerophon Find putative chimeras using bellerophon 6
Chimera.ccode Find putative chimeras using ccode 6
Chimera.check Find putative chimeras using chimeraCheck 6
Chimera.perseus Find putative chimeras using chimeraCheck 6
Chimera.pintail Find putative chimeras using pintail 6
Chimera.slayer Find putative chimeras using slayer 6
Chimera.uchime Find putative chimeras using uchime 6
Chimera.vsearch find potential chimeric sequences using vsearch 3
chips Codon usage statistics 4
ChIPseeker for ChIP peak annotation and visualization 5
Chop.seqs Trim sequences to a specified length 6
Circos visualizes data in a circular layout 6
Circos Builder creates circos plots from standard bioinformatics datatypes. 3
Circos: Alignments to links reformats alignment files to prepare for Circos 4
Circos: bigWig to Scatter reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots 4
Circos: Bundle Links reduce numbers of links in datasets before plotting 4
Circos: Interval to Circos Text Labels reformats interval files to prepare for Circos text labels 4
Circos: Interval to Tiles reformats interval files to prepare for Circos tile plots 4
Circos: Link Density Track reduce links to a density plot 4
Circos: Resample 1/2D data reduce numbers of points in a dataset before plotting 4
Circos: Table viewer easily creates circos plots from tabular data 4
cirdna Draws circular maps of DNA constructs 4
Classify.otu Assign sequences to taxonomy 6
Classify.rf description 2
Classify.seqs Assign sequences to taxonomy 6
Classify.tree Get a consensus taxonomy for each node on a tree 6
CleanSam perform SAM/BAM grooming 12
Clearcut Generate a tree using relaxed neighbor joining 6
Clip adapter sequences 5
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 7
ClosestBed find the closest, potentially non-overlapping interval 17
ClustalW multiple sequence alignment program for DNA or proteins 4
Cluster the intervals of a dataset Sequence clustering Sequence merging 5
Cluster Assign sequences to OTUs (Operational Taxonomic Unit) 6
Cluster OTU Cluster OTUs 1
Cluster.classic Assign sequences to OTUs (Dotur implementation) 6
Cluster.fragments Group sequences that are part of a larger sequence 6
Cluster.split Assign sequences to OTUs and split large matrices 5
ClusterBed cluster overlapping/nearby intervals 16
cmalign Align sequences to a covariance model against a sequence database 2
cmbuild Build covariance models from sequence alignments 3
CML to InChI 2
CML to mol2 2
CML to SDF 2
cmpress Prepare a covariance model database for cmscan 1
cmscan Search sequences against collections of covariance models 1
cmsearch Search covariance model(s) against a sequence database 2
cmstat Summary statistics for covariance model 2
codcmp Codon usage table comparison 4
coderet Extract CDS, mRNA and translations from feature tables 4
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 12
Collect.shared Generate collector's curves for calculators on OTUs 6
Collect.single Generate collector's curves for OTUs 7
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 12
CollectGcBiasMetrics charts the GC bias metrics 12
CollectHsMetrics compute metrics about datasets generated through hybrid-selection (e.g. exome) 3
CollectInsertSizeMetrics plots distribution of insert sizes 12
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 14
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 12
Column arrange by header name 2
Column Join on Collections 4
Column Regex Find And Replace 3
Combine FASTA and QUAL into FASTQ Aggregation 5
Compare BIOM tables Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples. 2
Compare two Datasets to find common or distinct rows 1
Complement intervals of a dataset Sequence coordinate conversion 4
ComplementBed Extract intervals not represented by an interval file 17
Compound conversion - interconvert between various chemistry and molecular modeling data files 4
compseq Count composition of dimer/trimer/etc words in a sequence 4
Compute an expression on every row 4
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 17
Compute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly 10
Compute Motif Frequencies in indel flanking regions 1
Compute Motif Frequencies For All Motifs motif by motif 1
Compute P-values and Correlation Coefficients for Feature Occurrences between two datasets using Discrete Wavelet Transfoms 1
Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features between two datasets using Discrete Wavelet Transfoms 1
Compute P-values and Max Variances for Feature Occurrences in one dataset using Discrete Wavelet Transfoms 1
Compute P-values and Second Moments for Feature Occurrences between two datasets using Discrete Wavelet Transfoms 1
Compute quality statistics 3
Compute sequence length 6
computeGCBias Determine the GC bias of your sequenced reads 16
computeMatrix prepares data for plotting a heatmap or a profile of given regions 17
computeMatrixOperations Modify or combine the output of computeMatrix in a variety of ways. 10
Concatenate two datasets into one dataset Aggregation 5
Concatenate FASTA alignment by species 2
Concatenate datasets tail-to-head 1
Concatenate datasets tail-to-head (cat) 7
Concatenate multiple datasets tail-to-head 3
Condense consecutive characters 2
Consensus.seqs Find a consensus sequence for each OTU or phylotype 6
Convert delimiters to TAB 1
Convert between BIOM table formats 3
Convert BCF to uncompressed BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 1
Convert CSV to tabular 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
Convert FASTA to fai file 1
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert from BAM to FastQ 13
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 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 Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 2
Convert SAM to interval 2
Convert SAM to BAM without sorting 1
Convert tabular to CSV 1
Convert tabular to dbnsfp 2
Convert tar to directory 2
Convert uncompressed BCF to BCF 1
Cooccurrence tests whether presence-absence patterns differ from chance 6
Corr.axes correlation of data to axes 6
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Correlation for numeric columns 1
Count occurrences of each record 2
Count GFF Features 2
Count.groups counts the number of sequences represented by a specific group or set of groups 6
Count.seqs (aka make.table) counts the number of sequences represented by the representative 6
Coverage of a set of intervals on second set of intervals Comparison Filtering 5
cpgplot Plot CpG rich areas 4
cpgreport Reports all CpG rich regions 4
Create assemblies with Unicycler Genome assembly 8
Create single interval as a new dataset 1
Create text file with recurring lines 8
Create.database creates a database file from a list, repnames, repfasta and contaxonomy file 5
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 9
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 10
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cuffmerge merge together several Cufflinks assemblies 8
Cuffnorm Create normalized expression levels 4
Cuffquant Precompute gene expression levels 4
cummeRbund visualize Cuffdiff output 2
cusp Create a codon usage table 4
Cut columns from a table 2
Cut columns from a table (cut) 8
cut_francais keep or remove selected column 1
Cutadapt Remove adapter sequences from Fastq/Fasta 16
cutseq Removes a specified section from a sequence 4
dan Calculates DNA RNA/DNA melting temperature 4
Data Fetch 1
Datamash (operations on tabular data) 3
Degap.seqs Remove gap characters from sequences 6
degapseq Removes gap characters from sequences 4
Deletion Profile calculates the distributions of deleted nucleotides across reads 3
Dereplicate Remove duplicate sequences 1
Describe samples and replicates 10
descseq Alter the name or description of a sequence 4
DESeq2 Determines differentially expressed features from count tables Differential gene expression analysis 18
Determine_batch_correction to choose between linear, lowess and loess methods 5
Deunique.seqs Return all sequences 6
Deunique.tree Reinsert the redundant sequence identiers back into a unique tree. 6
DEXSeq Determines differential exon usage from count tables 7
DEXSeq-Count Prepare and count exon abundancies from RNA-seq data 7
DiffBind differential binding analysis of ChIP-Seq peak data 12
Differential expression analysis using a Trinity assembly 11
Differential_Count models using BioConductor packages 1
diffseq Find differences between nearly identical sequences 4
digest Protein proteolytic enzyme or reagent cleavage digest 4
Dist.seqs calculate uncorrected pairwise distances between aligned sequences 6
Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups 6
dotmatcher Displays a thresholded dotplot of two sequences 4
dotpath Non-overlapping wordmatch dotplot of two sequences 4
dottup Displays a wordmatch dotplot of two sequences 4
Download and Extract Reads in BAM format from NCBI SRA 12
Download and Extract Reads in FASTA/Q format from NCBI SRA 13
Download and Generate Pileup Format from NCBI SRA 10
Downsample SAM/BAM Downsample a file to retain a subset of the reads 12
Draw nucleotides distribution chart 4
Draw quality score boxplot 5
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 4
edgeR Perform differential expression of count data 6
edgeR-repenrich Determines differentially expressed features from RepEnrich counts 2
EGSEA easy and efficient ensemble gene set testing 3
einverted Finds DNA inverted repeats 4
Ensemble methods for classification and regression 10
Enumerate changes calculated with Dimorphite DL and RDKit 2
epestfind Finds PEST motifs as potential proteolytic cleavage sites 4
equicktandem Finds tandem repeats 4
est2genome Align EST and genomic DNA sequences 4
Estimate substitution rates for non-coding regions 1
EstimateLibraryComplexity assess sequence library complexity from read sequences 12
etandem Looks for tandem repeats in a nucleotide sequence 4
ExpandBed replicate lines based on lists of values in columns 16
eXpress Quantify the abundances of a set of target sequences from sampled subsequences 2
Extract reads from a specified region 1
Extract and cluster differentially expressed transcripts from a Trinity assembly 11
Extract FASTQ in tabular format from a set of FAST5 files 2
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 8
Extract MAF blocks given a set of genomic intervals 1
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
extractfeat Extract features from a sequence 4
extractseq Extract regions from a sequence 4
Fasta Extract Sequence Extract a single sequence from a fasta file. 2
Fasta Statistics Display summary statistics for a fasta file. 2
FASTA Width formatter 3
FASTA-to-Tabular converter 4
Faster Download and Extract Reads in FASTQ format from NCBI SRA 2
fastp - fast all-in-one preprocessing for FASTQ files 6
FASTQ de-interlacer on paired end reads Splitting 5
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 6
FASTQ interlacer on paired end reads Aggregation 6
FASTQ joiner on paired end reads Aggregation 8
FASTQ Masker by quality score Sequence masking 5
FASTQ Quality Trimmer by sliding window 5
FASTQ splitter on joined paired end reads Splitting 5
FASTQ Summary Statistics by column Sequence assembly validation 4
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 5
FASTQ to Tabular converter Sequence conversion 6
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 19
FastqToSam convert Fastq data into unaligned BAM 15
FASTTREE build maximum-likelihood phylogenetic trees Phylogenetic tree analysis Phylogenetic tree generation (from molecular sequences) 6
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 18
Fetch closest non-overlapping feature for every interval Filtering 4
fgsea - fast preranked gene set enrichment analysis 3
Filter data on any column using simple expressions Formatting 1
Filter a VCF file 1
Filter by quality Filtering 5
Filter Combined Transcripts using tracking file 1
Filter FASTQ reads by quality score and length Filtering 6
Filter GFF data by attribute using simple expressions 3
Filter GFF data by feature count using simple expressions 2
Filter GTF data by attribute values_list 1
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 2
Filter SAM on bitwise flag values 2
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 6
Filter sequences by length Filtering 7
Filter.seqs removes columns from alignments 6
Filter.shared remove OTUs based on various critieria 6
FilterSamReads include or exclude aligned and unaligned reads and read lists 12
FisherBed calculate Fisher statistic between two feature files 16
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 12
FlankBed create new intervals from the flanks of existing intervals 17
Flye assembly of long and error-prone reads 3
Format tree and trait tables 2
FPKM Count calculates raw read count, FPM, and FPKM for each gene 5
freak Residue/base frequency table or plot 4
FreeBayes bayesian genetic variant detector 8
fuzznuc Nucleic acid pattern search 5
fuzzpro Protein pattern search 4
fuzztran Protein pattern search after translation 4
garnier Predicts protein secondary structure 4
GC Skew calculates skew over genomic sequences 4
geecee Calculates fractional GC content of nucleic acid sequences 4
GEMINI actionable_mutations Retrieve genes with actionable somatic mutations via COSMIC and DGIdb 3
GEMINI amend Amend an already loaded GEMINI database. 4
GEMINI annotate the variants in an existing GEMINI database with additional information 6
GEMINI autosomal recessive/dominant Find variants meeting an autosomal recessive/dominant model 3
GEMINI burden perform sample-wise gene-level burden calculations 3
GEMINI comp_hets Identifying potential compound heterozygotes 3
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 3
GEMINI dump Extract data from the Gemini DB 3
GEMINI fusions Identify somatic fusion genes from a GEMINI database 5
GEMINI gene_wise Discover per-gene variant patterns across families 3
GEMINI inheritance pattern based identification of candidate genes 2
GEMINI interactions Find genes among variants that are interacting partners 5
GEMINI load Loading a VCF file into GEMINI 7
GEMINI lof_sieve Filter LoF variants by transcript position and type 3
GEMINI mendel_errors Identify candidate violations of Mendelian inheritance 3
GEMINI pathways Map genes and variants to KEGG pathways 5
GEMINI qc Quality control tool 4
GEMINI query Querying the GEMINI database 4
GEMINI region Extracting variants from specific regions or genes 3
GEMINI roh Identifying runs of homozygosity 4
GEMINI set_somatic Tag somatic mutations in a GEMINI database 4
GEMINI stats Compute useful variant statistics 3
GEMINI windower Compute sliding window statistics from variants 4
Genbank to GFF3 converter 3
Genbank-to-Fasta produces a Fasta file from a genbank file 1
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 9
Gene Body Coverage (Bigwig) Read coverage over gene body 9
Generalized linear models for classification and regression 10
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 pileup from BAM dataset 3
Generic_Filter Removes elements according to numerical or qualitative values 4
Genome Coverage compute the coverage over an entire genome 17
Get flanks returns flanking region/s for every gene Sequence analysis 5
Get longest read from a set of FAST5 files. 2
Get PDB file from Protein Data Bank 2
Get.communitytype description 6
Get.coremicrobiome fraction of OTUs for samples or abundances 6
Get.dists selects distances from a phylip or column file 6
Get.group group names from shared or from list and group 6
Get.groups Select groups 6
Get.label label names from list, sabund, or rabund file 6
Get.lineage Picks by taxon 6
Get.mimarkspackage creates a mimarks package form with your groups 6
Get.otulabels Selects OTU labels 6
Get.otulist Get otus for each distance in a otu list 6
Get.oturep Generate a fasta with a representative sequence for each OTU 6
Get.otus Get otus containing sequences from specified groups 6
Get.rabund Get rabund from a otu list or sabund 6
Get.relabund Calculate the relative abundance of each otu 6
Get.sabund Get sabund from a otu list or rabund 6
Get.seqs Picks sequences by name 6
Get.sharedseqs Get shared sequences at each distance from list and group 6
GetFastaBed use intervals to extract sequences from a FASTA file 16
getorf Finds and extracts open reading frames (ORFs) 4
GFF-to-BED converter Conversion 1
GFF-to-BED converter 1
GffCompare compare assembled transcripts to a reference annotation 5
gffread Filters and/or converts GFF3/GTF2 records 6
GMAJ Multiple Alignment Viewer 1
Golm Metabolome Database search spectrum : GC-MS Mass Spectral Database. 2
goseq tests for overrepresented gene categories 8
GROMACS energy minimization of the system prior to equilibration and production MD 6
GROMACS initial setup of topology and GRO structure file 6
GROMACS simulation for system equilibration or data collection 5
GROMACS solvation and adding ions to structure and topology files 6
Group data by a column and perform aggregate operation on other columns. 5
GroupByBed group by common cols and summarize other cols 16
GTF-to-BEDGraph converter Conversion 1
GTF-to-GFF converter 1
Gubbins Recombination detection in Bacteria 1
Hcluster Assign sequences to OTUs (Operational Taxonomic Unit) 2
Heatmap w ggplot 2
Heatmap.bin Generate a heatmap for OTUs 6
Heatmap.sim Generate a heatmap for pariwise similarity 6
heatmap2 4
helixturnhelix Report nucleic acid binding motifs 4
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 3
HISAT2 A fast and sensitive alignment program 17
Histogram of a numeric column 2
HMDB MS search search by masses on HMDB online LCMS bank 3
hmoment Hydrophobic moment calculation 4
Homova Homogeneity of molecular variance 6
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
Hyperparameter Search performs hyperparameter optimization using various SearchCVs 9
HyPhy-aBSREL adaptive Branch Site Random Effects Likelihood 6
HyPhy-GARD Genetic Algorithm for Recombination Detection 6
IDR Consistency Analysis on a pair of narrowPeak files 1
IDR-Plot Plot Consistency Analysis on IDR output files 1
iep Calculates the isoelectric point of a protein 4
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
Indicator Identify indicator "species" for nodes on a tree 6
Infer Experiment speculates how RNA-seq were configured 9
infoseq Displays some simple information about sequences 4
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 9
Insertion Profile calculates the distribution of inserted nucleotides across reads 3
Intersect multiple VCF datasets 2
Intersect Generate the intersection of two VCF files 2
Intersect intervals find overlapping intervals in various ways 17
IQ-TREE Phylogenomic / evolutionary tree construction from multiple sequences 4
isochore Plots isochores in large DNA sequences 4
ivar consensus Call consensus from aligned BAM file 2
ivar filtervariants Filter variants across replicates or multiple samples aligned using the same reference 2
ivar getmasked Detect primer mismatches and get primer indices for the amplicon to be masked 2
ivar removereads Remove reads from trimmed BAM file 2
ivar trim Trim reads in aligned BAM 2
ivar variants Call variants from aligned BAM file 2
IWTomics Plot with Threshold on Test Scale 1
IWTomics Test and Plot 1
JaccardBed calculate the distribution of relative distances between two files 16
JBrowse genome browser 23
JBrowse - Data Directory to Standalone upgrades the bare data directory to a full JBrowse instance 22
Join the intervals of two datasets side-by-side Aggregation 5
Join two files 10
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
Junction Annotation compares detected splice junctions to reference gene model 9
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 9
Kallisto pseudo - run pseudoalignment on RNA-Seq transcripts 3
Kallisto quant - quantify abundances of RNA-Seq transcripts 5
KmerGenie k-mer histograms analysis 2
Kraken assign taxonomic labels to sequencing reads 7
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 2
LASTZ : align long sequences 4
Lastz paired reads map short paired reads against reference sequence 1
LASTZ_D : estimate substitution scores matrix 3
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. 5
Lefse description 6
Length Distribution chart 2
Libshuff Cramer-von Mises tests communities for the same structure 6
limma Perform differential expression with limma-voom or limma-trend 14
lindna Draws linear maps of DNA constructs 4
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 16
Lipidmaps : search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine. 1
List.otulabels Lists otu labels from shared or relabund file 6
List.seqs Lists the names (accnos) of the sequences 6
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 8
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 8
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 10
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 8
MACS2 callpeak Call peaks from alignment results Regulatory element prediction 12
MACS2 filterdup Remove duplicate reads at the same position Regulatory element prediction 8
MACS2 predictd Predict 'd' or fragment size from alignment results Regulatory element prediction 8
MACS2 randsample Randomly sample number or percentage of total reads Regulatory element prediction 8
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) Regulatory element prediction 8
MACS2.1.2 Model-based Analysis of ChIP-Seq: peak calling 2
MAF Coverage Stats Alignment coverage information 1
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 4
MAGeCK count - collect sgRNA read counts from read mapping files 7
MAGeCK GSEA - a fast implementation of Gene Set Enrichment Analysis 3
MAGeCK mle - perform maximum-likelihood estimation of gene essentiality scores 4
MAGeCK pathway - given a ranked gene list, test whether one pathway is enriched 3
MAGeCKs test - given a table of read counts, perform the sgRNA and gene ranking 4
Make Design Assign groups to Sets 6
Make.biom Make biom files from a shared file 6
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 6
Make.shared Make a shared file from a list and a group 7
Make.sra creates the necessary files for a NCBI submission 6
MakeWindowsBed make interval windows across a genome 17
MALDIquant peak detection Peak detection, binning and filtering for mass-spectrometry imaging data 6
MALDIquant preprocessing Preprocessing of mass-spectrometry imaging data 4
Manipulate FASTQ reads on various attributes Sequence conversion 5
Mantel Mantel correlation coefficient between two matrices. 6
Map Reads to OTU Maps read sequences to OTUs 1
Map with BWA - map short reads (< 100 bp) against reference genome 11
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 12
Map with minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences 9
MapBed apply a function to a column for each overlapping interval 17
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 13
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 12
marscan Finds MAR/SAR sites in nucleic sequences 4
MaskFastaBed use intervals to mask sequences from a FASTA file 16
maskfeat Mask off features of a sequence 4
maskseq Mask off regions of a sequence 4
MassBank spectrum searches : Search by pseudo-spectra on a High Quality Mass Spectral Database. 1
matcher Finds the best local alignments between two sequences 4
Max SuCOS score - determine maximum SuCOS score of ligands against clustered fragment hits 5
MeanQualityByCycle chart distribution of base qualities 12
MEGAHIT for metagenomics assembly 5
megamerger Merge two large overlapping nucleic acid sequences 4
Merge the overlapping intervals of a dataset Sequence merging 4
Merge multiple VCF datasets 2
Merge BAM Files merges BAM files together 3
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 16
Merge Columns together 2
Merge.count Merge count tables 3
Merge.files Merge data 6
Merge.groups Merge groups in a shared file 6
Merge.sfffiles Merge SFF files 6
Merge.taxsummary Merge tax.summary files 6
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 12
MergeBED combine overlapping/nearby intervals into a single interval 16
merger Merge two overlapping nucleic acid sequences 4
MergeSamFiles merges multiple SAM/BAM datasets into one 12
Metagenome Contributions of OTUs to user-specified functions 2
metaMS.runGC GC-MS data preprocessing using metaMS package 5
metaSPAdes assembler for metagenomics datasets 3
Metastats generate principle components plot data 6
Mimarks.attributes Reads bioSample Attributes xml and generates source for get.mimarkspackage command 6
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. 2
MiModD NacreousMap maps phenotypically selected variants by multi-variant linkage analysis 2
MiModD Rebase Sites from a VCF file 2
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 2
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 2
Mismatch Profile calculates the distribution of mismatches across reads 3
MLST Scans genomes against PubMLST schemes. 2
MLST List Lists available schemes for the MLST tool. 2
MOL to CML 2
MOL to MOL2 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
msbar Mutate sequence beyond all recognition 4
MSI classification spatial classification of mass spectrometry imaging data 4
MSI combine combine several mass spectrometry imaging datasets into one 5
MSI data exporter exports imzML and Analyze7.5 to tabular files 4
MSI filtering tool for filtering mass spectrometry imaging data 5
MSI mz images mass spectrometry imaging m/z heatmaps 4
MSI plot spectra mass spectrometry imaging mass spectra plots 5
MSI preprocessing mass spectrometry imaging preprocessing 5
MSI Qualitycontrol mass spectrometry imaging QC 6
MSI segmentation mass spectrometry imaging spatial clustering 5
MSnbase readMSData Imports mass-spectrometry data files 4
Multi-Join (combine multiple files) 8
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
MultiCovBed counts coverage from multiple BAMs at specific intervals 16
Multilevel Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package 1
Multiple Intersect identifies common intervals among multiple interval files 19
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 11
MUMmer dotplot Combine mummer/nucmer/promer with mummerplot 4
NanoFilt Filtering and trimming of long read sequencing data 1
NanoPlot Plotting suite for Oxford Nanopore sequencing data and alignments 5
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. 2
Nanopolish variants - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences 3
NCBI Accession Download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 1
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 16
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 13
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 16
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 14
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 17
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 11
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 13
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
needle Needleman-Wunsch global alignment 4
newcpgreport Report CpG rich areas 4
newcpgseek Reports CpG rich region 4
newseq Type in a short new sequence 4
Nmds generate non-metric multidimensional scaling data 6
NMR spectra alignment based on the Cluster-based Peak Alignment (CluPA) algorithm 3
NMR_Bucketing Bucketing and integration of NMR Bruker raw data 5
NMR_Preprocessing Preprocessing of 1D NMR spectra 3
NMR_Read Read Bruker NMR raw files 2
noreturn Removes carriage return from ASCII files 4
Normalization Normalization of (preprocessed) spectra 4
Normalize the relative abundance of each OTU by the predicted number of 16S copies 3
Normalize.shared Normalize the number of sequences per group to a specified level 6
NormalizeFasta normalize fasta datasets 12
notseq Exclude a set of sequences and write out the remaining ones 4
nthseq Writes one sequence from a multiple set of sequences 4
NucBed profile the nucleotide content of intervals in a FASTA file 17
octanol Displays protein hydropathy 4
oddcomp Find protein sequence regions with a biased composition 4
OPLS-DA_Contrasts OPLS-DA Contrasts of Univariate Results 4
Otu.association Calculate the correlation coefficient for the otus 6
Otu.hierarchy Relate OTUs at different distances 6
OverlapBed computes the amount of overlap from two intervals 16
Pairwise.seqs calculate uncorrected pairwise distances between sequences 6
palindrome Looks for inverted repeats in a nucleotide sequence 4
Parallel Coordinates Plot of tabular data 3
Parse.list Generate a List file for each group 6
Parsimony Describes whether two or more communities have the same structure 6
Partition genes into expression clusters after differential expression analysis using a Trinity assembly 11
Paste two files side by side 1
pasteseq Insert one sequence into another 4
patmatdb Search a protein sequence with a motif 4
Pca Principal Coordinate Analysis for a shared file 6
PCA - principal component analysis using Bio3D 2
Pcoa Principal Coordinate Analysis for a distance matrix 5
Pcr.seqs Trim sequences 6
Pear Paired-End read merger 4
pepcoil Predicts coiled coil regions 4
pepinfo Plots simple amino acid properties in parallel 4
pepnet Displays proteins as a helical net 4
pepstats Protein statistics 4
pepwheel Shows protein sequences as helices 4
pepwindow Displays protein hydropathy 4
pepwindowall Displays protein hydropathy of a set of sequences 4
Phylo.diversity Alpha Diversity calculates unique branch length 6
Phyloseq Biom Filtering biom file filter 1
Phyloseq Ordination Plot ordination plotting 1
Phylotype Assign sequences to OTUs based on taxonomy 6
PhyML Phylogeny software based on the maximum-likelihood Phylogenetic tree analysis Phylogenetic tree generation (from molecular sequences) 5
Phyogenetic reconstruction with RaXML - Maximum Likelihood based inference of large phylogenetic trees 4
Picard Collect Sequencing Artifact Metrics Collect metrics to quantify single-base sequencing artifacts 3
Pileup-to-Interval condenses pileup format into ranges of bases 4
pilon An automated genome assembly improvement and variant detection tool 2
Pipeline Builder an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers 9
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 4
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 2
plotEnrichment plots read/fragment coverage over sets of regions 12
plotFingerprint plots profiles of BAM files; useful for assessing ChIP signal strength 17
plotHeatmap creates a heatmap for score distributions across genomic regions 17
plotorf Plot potential open reading frames 4
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 3
Poisson two-sample test 1
polydot Displays all-against-all dotplots of a set of sequences 4
Porechop adapter trimmer for Oxford Nanopore reads 1
Pre.cluster Remove sequences due to pyrosequencing errors 6
Predict Metagenome based on the abundance of OTUs and a functional database 3
preg Regular expression search of a protein sequence 4
prettyplot Displays aligned sequences, with colouring and boxing 4
prettyseq Output sequence with translated ranges 4
Primer.design identify sequence fragments that are specific to particular OTUs 6
primersearch Searches DNA sequences for matches with primer pairs 4
ProbMetab Tool Wrapper function for ProbMetab R package. 3
proFIA Preprocessing of FIA-HRMS data 4
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 8
proportional venn from 2-3 sets 1
PyNAST PyNAST is a reimplementation of the NAST sequence aligner for adding new 16S rDNA sequences to existing 16S rDNA alignments. 1
QualiMap BamQC 3
QualiMap Multi-Sample BamQC 2
QualiMap RNA-Seq QC 3
Quality format converter (ASCII-Numeric) 3
Quality Metrics Metrics and graphics to check the quality of the data 4
QualityScoreDistribution chart quality score distribution 12
Quast Genome assembly Quality 8
Racon Consensus module for raw de novo DNA assembly of long uncorrected reads. 2
RandomBed generate random intervals in a genome 17
Rarefaction Calculate and plot rarefaction curves 1
Rarefaction.shared Generate inter-sample rarefaction curves for OTUs 6
Rarefaction.single Generate intra-sample rarefaction curves for OTUs 6
rDock cavity definition - generate the active site definition needed for rDock docking 2
rDock docking - perform protein-ligand docking with rDock 5
Read Distribution calculates how mapped reads were distributed over genome feature 9
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 7
Read GC determines GC% and read count 7
Read length statistics from a set of FAST5 files 2
Read NVC to check the nucleotide composition bias 7
Read Quality determines Phred quality score 7
Realign reads with LoFreq viterbi 3
Regex Find And Replace 2
Reheader copy SAM/BAM header between datasets 2
ReldistBed calculate the distribution of relative distances 16
Remove beginning of a file 1
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 6
Remove.lineage Picks by taxon 6
Remove.otulabels Removes OTU labels 5
Remove.otus Removes OTUs from various file formats 6
Remove.rare Remove rare OTUs 6
Remove.seqs Remove sequences by name 6
Rename sequences 5
Rename.seqs Rename sequences by concatenating the group name 3
ReorderSam reorder reads to match ordering in reference sequences 15
RepEnrich Repeat Element Profiling 2
Replace parts of text 9
Replace Text in entire line 8
Replace Text in a specific column 8
ReplaceSamHeader replace header in a SAM/BAM dataset 15
Reverse Complement a MAF file 1
Reverse-Complement 5
Reverse.seqs Reverse complement the sequences 6
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 12
RevertSam revert SAM/BAM datasets to a previous state 12
revseq Reverse and complement a sequence 4
RmDup remove PCR duplicates 7
RMSD Analysis using Bio3D 2
RMSF Analysis using Bio3D 2
RNA fragment size calculates the fragment size for each gene/transcript 5
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly 13
RNA/DNA converter 5
RnaChipIntegrator Integrated analysis of 'gene' and 'peak' data 3
RNASeq samples quality check for transcript quantification 11
Roary the pangenome pipeline - Quickly generate a core gene alignment from gff3 files 5
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 9
RSEM calculate expression RNA-Seq by Expectation-Maximization 1
RSEM prepare reference 1
RSEM trinity fasta to gene map extract transcript to gene map from trinity 3
Sailfish transcript quantification from RNA-seq data 4
Salmon Transcript Quantification from RNA-seq data 8
SAM-to-BAM convert SAM to BAM 11
SAM/BAM to count matrix using HTSeq code 1
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 17
Samtools fastx extract FASTA or FASTQ from alignment files 2
Samtools flagstat tabulate descriptive stats for BAM datset 8
Samtools idxstats reports stats of the BAM index file 8
samtools mpileup multi-way pileup of variants 9
Samtools sort order of storing aligned sequences 7
Samtools stats generate statistics for BAM dataset 7
Screen.seqs Screen sequences 6
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
Search in textfiles (grep) 7
Secure Hash / Message Digest on a dataset 2
Select lines that match an expression 1
Select first lines from a dataset 1
Select first lines from a dataset (head) 8
Select last lines from a dataset 1
Select last lines from a dataset (tail) 8
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 6
seqmatchall All-against-all comparison of a set of sequences 4
seqret Reads and writes sequences 4
Sequence Logo generator for fasta (eg Clustal alignments) 3
SFF converter 1
Sffinfo Summarize the quality of sequences 6
Shhh.flows Denoise flowgrams (PyroNoise algorithm) 6
Shhh.seqs Denoise program (Quince SeqNoise) 6
Shovill Faster SPAdes assembly of Illumina reads 5
Show nucleotide distribution in nanopore sequencing reads 2
Show quality score distribution in nanopore sequencing reads 2
showfeat Show features of a sequence 4
ShuffleBed randomly redistrubute intervals in a genome 17
shuffleseq Shuffles a set of sequences maintaining composition 4
SICER Statistical approach for the Identification of ChIP-Enriched Regions 2
sigcleave Reports protein signal cleavage sites 4
sirna Finds siRNA duplexes in mRNA 4
sistr_cmd Salmonella In Silico Typing Resource commandline tool for serovar prediction 1
sixpack Display a DNA sequence with 6-frame translation and ORFs 6
skipseq Reads and writes sequences, skipping first few 4
Slice BAM by genomic regions 5
Slice VCF to get data from selected regions 1
SlopBed adjust the size of intervals 18
snippy Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 9
snippy-clean_full_aln Replace any non-standard sequence characters in snippy 'core.full.aln' file. 2
snippy-core Combine multiple Snippy outputs into a core SNP alignment 8
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 10
SnpEff chromosome-info: list chromosome names/lengths 4
SnpEff databases: list available databases 12
SnpEff download: download a pre-built database 12
SnpEff eff: annotate variants 14
snpFreq significant SNPs in case-control data 1
SnpSift Annotate SNPs from dbSnp 7
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 7
SnpSift Extract Fields from a VCF file into a tabular file 5
SnpSift Filter Filter variants using arbitrary expressions 7
SnpSift Intervals Filter variants using intervals 7
SnpSift rmInfo remove INFO field annotations 6
SnpSift Variant Type Annotate with variant type 6
SnpSift vcfCheck basic checks for VCF specification compliance 6
Sort data in ascending or descending order 2
Sort data in ascending or descending order 7
Sort a row according to their columns 8
Sort.seqs put sequences in different files in the same order 6
SortBED order the intervals 16
SortSam sort SAM/BAM dataset 12
SpacingBed reports the distances between features 12
SPAdes genome assembler for regular and single-cell projects Genome assembly 11
Split BAM dataset on readgroups 3
Split file to dataset collection 4
Split MAF blocks by Species 1
Split paired end reads 1
Split.abund Separate sequences into rare and abundant groups 6
Split.groups Generates a fasta file for each group 6
splitter Split a sequence into (overlapping) smaller sequences 4
SPP SPP cross-correlation analysis package 1
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 13
StringTie merge transcripts 7
Sub.sample Create a sub sample 6
Subset columns from a VCF dataset 1
Subtract the intervals of two datasets Filtering 5
Subtract Whole Dataset from another dataset 3
SubtractBed remove intervals based on overlaps 16
Summary Statistics for any numerical column 3
Summary.qual Summarize the quality scores 6
Summary.seqs Summarize the quality of sequences 6
Summary.shared Summary of calculator values for OTUs 5
Summary.single Summary of calculator values for OTUs 7
Summary.tax Assign sequences to taxonomy 6
supermatcher Match large sequences against one or more other sequences 4
Support vector machines (SVMs) for classification 9
syco Synonymous codon usage Gribskov statistic plot 4
T Test for Two Samples 2
Table Compute computes operations on table data 1
Table Merge Merging dataMatrix with a metadata table 3
Tabular to FASTQ converter Conversion 6
Tabular-to-FASTA converts tabular file to FASTA format 3
tac reverse a file (reverse cat) 8
TagBed tag BAM alignments based on overlaps with interval files 16
Taxonomy-to-Krona convert a mothur taxonomy file to Krona input format 3
tcode Fickett TESTCODE statistic to identify protein-coding DNA 4
Text reformatting with awk 7
Text transformation with sed 7
textsearch Search sequence documentation. Slow, use SRS and Entrez! 4
tmap Displays membrane spanning regions 4
TopHat Gapped-read mapper for RNA-seq data 10
Tophat Fusion Post post-processing to identify fusion genes 1
TRAMS Tool for Rapid Annotation of Microbial SNPs 1
tranalign Align nucleic coding regions given the aligned proteins 4
Transcript Integrity Number evaluates RNA integrity at a transcript level 5
TransDecoder Find coding regions within transcripts 4
transeq Translate nucleic acid sequences 4
Tree.shared Generate a newick tree for dissimilarity among groups 6
Trim leading or trailing characters 1
Trim Galore! Quality and adapter trimmer of reads 8
Trim sequences 5
Trim.flows partition by barcode, trim to length, cull by length and mismatches 6
Trim.seqs Trim sequences - primers, barcodes, quality 6
trimest Trim poly-A tails off EST sequences 4
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 14
trimseq Trim ambiguous bits off the ends of sequences 4
Trinity de novo assembly of RNA-Seq data 12
Trinotate 2
tRNA and tmRNA prediction (Aragorn) 3
tRNA prediction (tRNAscan) 2
twofeat Finds neighbouring pairs of features in sequences 4
Uchime Detecting chimeric sequences with two or more segments. 1
Unfold columns from a table 7
unifrac.unweighted Describes whether two or more communities have the same structure 6
unifrac.weighted Describes whether two or more communities have the same structure 6
union Reads sequence fragments and builds one sequence 4
Unique occurrences of each record 8
Unique lines assuming sorted input file 7
Unique.seqs Return unique sequences 6
Univariate Univariate statistics 4
Upload File from your computer 2
ValidateSamFile assess validity of SAM/BAM dataset 12
VarScan for variant detection 3
VCF to MAF Custom Track for display at UCSC 2
VCF-BEDintersect: Intersect VCF and BED datasets 6
VCF-VCFintersect: Intersect two VCF datasets 7
VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset 7
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 6
VCFannotate: Intersect VCF records with BED annotations 6
VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset 7
VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 6
VCFcheck: Verify that the reference allele matches the reference genome 6
VCFcombine: Combine multiple VCF datasets 7
VCFcommonSamples: Output records belonging to samples common between two datasets 6
VCFdistance: Calculate distance to the nearest variant 6
VCFfilter: filter VCF data in a variety of attributes 7
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 7
VCFgenotypes: Convert numerical representation of genotypes to allelic 6
VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio 6
VCFleftAlign: Left-align indels and complex variants in VCF dataset 6
VCFprimers: Extract flanking sequences for each VCF record 5
VCFrandomSample: Randomly sample sites from VCF dataset 7
VCFselectsamples: Select samples from a VCF dataset 7
VCFsort: Sort VCF dataset by coordinate 5
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 8
vectorstrip Strips out DNA between a pair of vector sequences 4
velvet 1
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 6
Visualize with Krona Visualise any hierarchical data 2
Volcano Plot create a volcano plot 3
VSearch alignment Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch chimera detection Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch clustering Chimeric sequence detection Sequence clustering Sequence masking 6
VSearch dereplication Chimeric sequence detection Sequence clustering Sequence masking 6
VSearch masking Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch search Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch shuffling Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch sorting Chimeric sequence detection Sequence clustering Sequence masking 6
W4m Data Subset Filter W4m data by values or metadata 8
water Smith-Waterman local alignment 4
Wavelet variance using Discrete Wavelet Transfoms 2
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2
WindowBed find overlapping intervals within a window around an interval 16
wobble Wobble base plot 4
wordcount Counts words of a specified size in a DNA sequence 4
wordmatch Finds all exact matches of a given size between 2 sequences 4
xcms adjustRtime (retcor) Retention Time Correction 11
xcms fillChromPeaks (fillPeaks) Integrate areas of missing peaks 14
xcms findChromPeaks (xcmsSet) Chromatographic peak detection 14
xcms findChromPeaks Merger Merge xcms findChromPeaks RData into a unique file to be used by group 6
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. 13
xcms plot chromatogram Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) 4
xcms process history Create a summary of XCMS analysis 8