Examples : samtools, bed, topic:conversion

742 tool(s) found

Tool Description Topics Available version(s)
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
Add column to an existing dataset Editing 2
AddCommentsToBam add comments to BAM dataset 14
Adding New Topology Information to a GROMACS topology file 1
AddOrReplaceReadGroups add or replaces read group information 14
Aggregate datapoints Appends the average, min, max of datapoints per interval 2
Align sequences using a variety of alignment methods (align_seqs) 2
Align.check Calculate the number of potentially misaligned bases 6
Align.seqs Align sequences to a template alignment 5
alignmentsieve Filter BAM/CRAM files according to specified parameters 7
Amova Analysis of molecular variance 5
Analyze statistical significance of sample groupings using distance matrices (compare_categories) 2
Angle Analysis - time series of Angles 5
Annotate DESeq2/DEXSeq output tables Append annotation from GTF to differential expression tool outputs 2
Anosim Non-parametric multivariate analysis of changes in community structure 5
Apply Variant Recalibration 3
Assign taxonomy to each sequence (assign_taxonomy) 2
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
BAM-to-SAM convert BAM to SAM 5
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
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 16
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 1
Base Recalibrator calculates covariates used to recalibrate base quality scores of reads 3
bcf_uncompressed-to-bcf converter 1
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BedCov calculate read depth for a set of genomic intervals 5
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
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
Bin.seqs Order Sequences by OTU 5
Biom.info create shared and taxonomy files from biom 2
Bismark Deduplicate Deduplicates reads mapped by Bismark 9
Bismark Mapper Bisulfite reads mapper 15
Bismark Meth. Extractor Reports on methylation status of reads mapped by Bismark 11
Bismark Pretty Report Generates a graphical HTML report page from report outputs of Bismark 9
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 18
Bowtie2 - map reads against reference genome 21
Boxplot of quality statistics 2
BSMAP Mapper 1
BSMAP Methylation Caller 1
Build a UPGMA tree comparing samples (upgma_cluster) 2
Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity) 2
Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables (beta_diversity) 2
calculate pore diameter of AQP 1
cd-hit Cluster or compare biological sequence datasets 2
Centrifuge Read-based metagenome characterization 1
Change Case of selected columns 2
Check user's metadata mapping file for required data, valid format (validate_mapping_file) 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
Chop.seqs Trim sequences to a specified length 6
Classify.otu Assign sequences to taxonomy 5
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
Clip adapter sequences 6
Closed-reference OTU picking Shotgun UniFrac workflow (pick_closed_reference_otus) 2
ClustalW multiple sequence alignment program for DNA or proteins 5
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
CML to InChI 2
CML to mol2 2
CML to SDF 2
cml-to-smi converter 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
CollectInsertSizeMetrics plots distribution of insert sizes 14
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
Combine Variants 3
Compare two Datasets to find common or distinct rows Filtering 1
Compound conversion - interconvert between various chemistry and molecular modeling data files 6
Compute on rows 10
Compute beta diversity distance matrices and generate PCoA plots (beta_diversity_through_plots) 2
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 21
Compute quality statistics 3
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 datasets tail-to-head Aggregation 1
Concatenate datasets tail-to-head (cat) 11
concatenate lines of multi tables 1
Consensus.seqs Find a consensus sequence for each OTU or phylotype 6
Convert delimiters to TAB 1
Convert Amber topology and coordinate files to GROMACS format using acpype 1
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 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 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
Cooccurrence tests whether presence-absence patterns differ from chance 6
Corr.axes correlation of data to axes 5
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Cosine Content - measure the cosine content of the PCA projection 4
Count occurrences of each record 2
Count the sequences in a fasta file (count_seqs) 2
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
Create GROMACS index files using make_ndx 4
Create GROMACS position restraints files using genrestr 4
Create single interval as a new dataset 1
Create text file with recurring lines 9
Create three-dimensional PCoA plots to be visualized with Emperor (make_emperor) 2
Create.database creates a database file from a list, repnames, repfasta and contaxonomy file 5
csv-to-tabular converter 1
Cut columns from a table Filtering 2
Cut columns from a table (cut) 9
cut trajectory 1
Cutadapt Remove adapter sequences from FASTQ/FASTA Sequence editing 22
Cytosine Report To Bedgraphs Converts genome-wide cytosine methylation report to Bedgraphs 1
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
DCCM analysis - Dynamical Cross-Correlation Maps using Bio3D (DCCM) 2
Degap.seqs Remove gap characters from sequences 5
Depth of Coverage on BAM files 3
DESeq2 Determines differentially expressed features from count tables Differential gene expression profiling RNA-Seq quantification 22
Deunique.seqs Return all sequences 5
Deunique.tree Reinsert the redundant sequence identiers back into a unique tree. 5
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
Differential_Count models using BioConductor packages 2
Dihedral Analysis Time series of dihedrals 5
Dist.seqs calculate uncorrected pairwise distances between aligned sequences 5
Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups 5
Distance Analysis - time series using MDAnalysis 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
Download and Generate Pileup Format from NCBI SRA 9
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
Draw nucleotides distribution chart 4
DREME - Discriminative Regular Expression Motif Elicitation 4
edgeR Perform differential expression of count data Differential gene expression profiling RNA-seq read count analysis 10
End-to-End Analysis - End-to-End distance timeseries and histogram for the given selections 2
estimate number of sub-trajectories 1
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
estimateReadFiltering estimates the number of reads that would be filtered given certain criteria 6
Eval Variants 3
Extract energy components with GROMACS 7
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
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 Pairwise MAF blocks given a set of genomic intervals 1
Extract RMSD distance matrix data from MD ensemble with MDAnalysis 3
Extracting Topology Information from a GROMACS topology file 1
Fasta Statistics Display summary statistics for a fasta file. 5
fasta-to-fai converter 1
fastp - fast all-in-one preprocessing for FASTQ files 8
FASTQ interlacer on paired end reads Aggregation 6
Fastq.info Convert fastq to fasta and quality 6
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
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
Filter data on any column using simple expressions Formatting 2
Filter fasta to remove sequences based on input criteria (filter_fasta) 2
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 MAF by specified attributes 1
Filter MAF blocks by Species 1
Filter MAF blocks by Size 1
Filter OTUs from an OTU table based on their observation counts or identifier (filter_otus_from_otu_table) 2
Filter SAM or BAM files on FLAG MAPQ RG LN or by region Filtering Nucleic acid sequence analysis 2
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 6
Filter sequence alignment by removing highly variable regions (filter_alignment) 2
Filter taxa from an OTU table (filter_taxa_from_otu_table) 2
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
Filters samples from an OTU table on the basis of the number of observations in that sample, or on the basis of sample metadata (filter_samples_from_otu_table) 2
FilterSamReads include or exclude aligned and unaligned reads and read lists 14
FIMO - Scan a set of sequences for motifs 12
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 14
Format Fastq sequences and barcode data (extract_barcodes) 2
FROGS Abundance normalisation Normalize OTUs abundance. Standardisation and normalisation 5
FROGS Affiliation Filters Filters OTUs on several affiliation criteria 3
FROGS Affiliation OTU Taxonomic affiliation of each OTU's seed by RDPtools and BLAST Taxonomic classification 5
FROGS Affiliation postprocess Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics Taxonomic classification 5
FROGS Affiliations stat Process some metrics on taxonomies. Taxonomic classification 5
FROGS BIOM to std BIOM Converts a FROGS BIOM in fully compatible BIOM. Formatting 5
FROGS BIOM to TSV Converts a BIOM file in TSV file. Formatting 5
FROGS Clustering swarm Single-linkage clustering on sequences Taxonomic classification 5
FROGS Clusters stat Process some metrics on clusters. Clustering 5
FROGS Demultiplex reads Attribute reads to samples in function of inner barcode. Classification 5
FROGS ITSx Extract the highly variable ITS1 and ITS2 subregions from ITS sequences. Sequence trimming 5
FROGS OTU Filters Filters OTUs on several criteria. 3
FROGS Pre-process merging, denoising and dereplication. Filtering 5
FROGS Remove chimera Remove PCR chimera in each sample. Editing 5
FROGS Tree Reconstruction of phylogenetic tree Taxonomic classification 5
FROGS TSV_to_BIOM Converts a TSV file in a BIOM file. Formatting 5
FROGSFUNC_step1_placeseqs Places the OTUs into a reference phylogenetic tree. 2
FROGSFUNC_step2_copynumbers Predicts number of marker and function copy number in each OTU. 2
FROGSFUNC_step3_functions Calculates functions abundances in each sample. 2
FROGSFUNC_step4_pathways Calculates pathway abundances in each sample. 2
FROGSSTAT DESeq2 Preprocess import a Phyloseq object and prepare it for DESeq2 differential abundance analysis 3
FROGSSTAT Phyloseq Alpha Diversity with richness plot Taxonomic classification 5
FROGSSTAT Phyloseq Beta Diversity distance matrix Taxonomic classification 5
FROGSSTAT Phyloseq Composition Visualisation with bar plot and composition plot Taxonomic classification 5
FROGSSTAT Phyloseq Import Data from 3 files: biomfile, samplefile, treefile Taxonomic classification 5
FROGSSTAT Phyloseq Multivariate Analysis Of Variance perform Multivariate Analysis of Variance (MANOVA) Taxonomic classification 5
FROGSSTAT Phyloseq Sample Clustering of samples using different linkage methods Taxonomic classification 5
FROGSSTAT Phyloseq Structure Visualisation with heatmap plot and ordination plot Taxonomic classification 5
FROGSTAT Deseq2 Visualisation to extract and visualise differentially abundant OTUs 3
g:Profiler tools for functional profiling of gene lists 1
Gene BED To Exon/Intron/Codon BED expander 1
Generate MD topologies for small molecules using acpype 9
Get Microbial Data Query and retrieval 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
GFF-to-BED converter Conversion 1
gffread Filters and/or converts GFF3/GTF2 records 7
GROMACS check to provide information about GROMACS input files 2
GROMACS copy file from built-in datasets 2
GROMACS energy minimization of the system prior to equilibration and production MD 7
GROMACS initial setup of topology and GRO structure file 6
GROMACS NPT equilibration - constant-temperature and -pressure equilibration of a system 2
GROMACS NVT equilibration - constant-temperature and -volume equilibration of a system 2
GROMACS production simulation for data collection 2
GROMACS Radius of Gyration of a molecular structure 2
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
GTF-to-BEDGraph converter Conversion 1
Haplotype Caller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region 3
Heatmap.bin Generate a heatmap for OTUs 5
Heatmap.sim Generate a heatmap for pariwise similarity 5
HISAT2 A fast and sensitive alignment program 19
Homova Homogeneity of molecular variance 5
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
Hydrogen Bond Analysis - analyze H-bonds between two segments 4
IdxStats reports stats of the BAM index file 8
InChI to CML 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
inchi-to-mol converter 2
Indel Realigner - perform local realignment 3
Indicator Identify indicator "species" for nodes on a tree 5
Intersect intervals find overlapping intervals in various ways 22
IQ-TREE Phylogenomic / evolutionary tree construction from multiple sequences 7
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
Join two files 12
Join the intervals of two datasets side-by-side Aggregation 5
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 4
Kraken-report view sample report of a classification 5
Kraken2 assign taxonomic labels to sequencing reads 5
Krona pie chart from taxonomic profile 10
LASTZ : align long sequences 7
LASTZ_D : estimate substitution scores matrix 5
LAV to BED Converts a LAV formatted file to BED format 1
LD linkage disequilibrium and tag SNPs 1
Lefse description 5
Libshuff Cramer-von Mises tests communities for the same structure 5
Line/Word/Character count of a dataset 1
List.otulabels Lists otu labels from shared or relabund file 5
List.seqs Lists the names (accnos) of the sequences 5
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
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
Make Design Assign groups to Sets 5
Make phylogeny (make_phylogeny) 2
Make taxonomy summary charts based on taxonomy assignment (plot_taxa_summary) 2
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
Mantel Mantel correlation coefficient between two matrices. 5
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
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
MeanQualityByCycle chart distribution of base qualities 14
Megablast compare short reads against htgs, nt, and wgs databases 2
MEGAHIT for metagenomics assembly 7
MEME - Multiple EM for Motif Elicitation 10
MEME psp-gen - perform discriminative motif discovery 6
MEME-ChIP - motif discovery, enrichment analysis and clustering on large nucleotide datasets 3
Merge Columns together 4
merge feature table and taxonomy - Merge features and taxonomy into a single biom file. 1
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
MergeSamFiles merges multiple SAM/BAM datasets into one 14
MetaGeneAnnotator gene-finding program for prokaryote and phage (used by sixgill) 1
Metastats generate principle components plot data 5
methylKit DNA methylation analysis and annotation 1
metilene calling differentially methylated regions from bisulfite sequencing data 5
Mimarks.attributes Reads bioSample Attributes xml and generates source for get.mimarkspackage command 5
MiRDeep2 identification of novel and known miRNAs 3
Modify/convert GROMACS trajectories using trjconv and trjcat 8
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to SDF 2
MOL2 to SMILES 2
mol2-to-mol converter 2
mothur.ref.taxonomy-to-mothur.seq.taxonomy converter 2
msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report 1
MSstats statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry 5
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
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 18
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
Nmds generate non-metric multidimensional scaling data 6
Normalize.shared Normalize the number of sequences per group to a specified level 5
NormalizeFasta normalize fasta datasets 14
NucBed profile the nucleotide content of intervals in a FASTA file 21
Otu.association Calculate the correlation coefficient for the otus 5
Otu.hierarchy Relate OTUs at different distances 5
Pairwise.seqs calculate uncorrected pairwise distances between sequences 5
Parse blast XML output 2
Parse.list Generate a List file for each group 5
Parsimony Describes whether two or more communities have the same structure 5
Paste two files side by side 1
Pca Principal Coordinate Analysis for a shared file 6
PCA - principal component analysis using Bio3D 2
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
Perform alpha rarefaction (alpha_rarefaction) 2
Perform jackknifed UPGMA clustering and building jackknifed PCoA plots (jackknifed_beta_diversity) 2
Perform open-reference OTU picking (pick_open_reference_otus) 2
Perform OTU picking (pick_otus) 2
Perform taxonomy summaries and plots (summarize_taxa_through_plots) 2
Phylo.diversity Alpha Diversity calculates unique branch length 5
Phylotype Assign sequences to OTUs based on taxonomy 5
Pick representative set of sequences (pick_rep_set) 2
PlasFlow Prediction of plasmid sequences in metagenomic contigs 1
Plot heatmap of OTU table (make_otu_heatmap) 2
plotCorrelation Create a heatmap or scatterplot of correlation scores between different samples 16
plotCoverage assesses the sequencing depth of BAM/CRAM files 16
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
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
Pre.cluster Remove sequences due to pyrosequencing errors 5
Primer.design identify sequence fragments that are specific to particular OTUs 5
Print Reads on BAM files 3
proportional venn from 2-3 sets 1
qiime alignment mafft - De novo multiple sequence alignment with MAFFT 1
qiime alignment mask - Positional conservation and gap filtering. 1
qiime composition add-pseudocount - Add pseudocount to table 1
qiime composition ancom - Apply ANCOM to identify features that differ in abundance. 1
qiime cutadapt demux-paired - Demultiplex paired-end sequence data with barcodes in- sequence. 1
qiime cutadapt demux-single - Demultiplex single-end sequence data with barcodes in- sequence. 1
qiime cutadapt trim-paired - Find and remove adapters in demultiplexed paired-end sequences. 1
qiime cutadapt trim-single - Find and remove adapters in demultiplexed single-end sequences. 1
qiime dada2 denoise-paired - Denoise and dereplicate paired-end sequences 1
qiime dada2 denoise-pyro - Denoise and dereplicate single-end pyrosequences 1
qiime dada2 denoise-single - Denoise and dereplicate single-end sequences 1
qiime deblur denoise-16S - Deblur sequences using a 16S positive filter. 1
qiime deblur denoise-other - Deblur sequences using a user-specified positive filter. 1
qiime deblur visualize-stats - Visualize Deblur stats per sample. 1
qiime demux emp-paired - Demultiplex paired-end sequence data generated with the EMP protocol. 1
qiime demux emp-single - Demultiplex sequence data generated with the EMP protocol. 1
qiime demux summarize - Summarize counts per sample. 1
qiime diversity alpha - Alpha diversity 1
qiime diversity alpha-correlation - Alpha diversity correlation 1
qiime diversity alpha-group-significance - Alpha diversity comparisons 1
qiime diversity alpha-phylogenetic - Alpha diversity (phylogenetic) 1
qiime diversity alpha-rarefaction - Alpha rarefaction curves 1
qiime diversity beta - Beta diversity 1
qiime diversity beta-group-significance - Beta diversity group significance 1
qiime diversity beta-phylogenetic - Beta diversity (phylogenetic) 1
qiime diversity beta-phylogenetic-alt - Beta diversity (phylogenetic) - High Performance Computation 1
qiime diversity beta-rarefaction - Beta diversity rarefaction 1
qiime diversity bioenv - bioenv 1
qiime diversity core-metrics - Core diversity metrics (non-phylogenetic) 1
qiime diversity core-metrics-phylogenetic - Core diversity metrics (phylogenetic and non- phylogenetic) 1
qiime diversity filter-distance-matrix - Filter samples from a distance matrix. 1
qiime diversity mantel - Apply the Mantel test to two distance matrices 1
qiime diversity pcoa - Principal Coordinate Analysis 1
qiime diversity procrustes-analysis - Procrustes Analysis 1
qiime emperor plot - Visualize and Interact with Principal Coordinates Analysis Plots 1
qiime emperor procrustes-plot - Visualize and Interact with a procrustes plot 1
qiime feature-classifier classify-consensus-blast - BLAST+ consensus taxonomy classifier 1
qiime feature-classifier classify-consensus-vsearch - VSEARCH consensus taxonomy classifier 1
qiime feature-classifier classify-sklearn - Pre-fitted sklearn-based taxonomy classifier 1
qiime feature-classifier extract-reads - Extract reads from reference 1
qiime feature-classifier fit-classifier-naive-bayes - Train the naive_bayes classifier 1
qiime feature-classifier fit-classifier-sklearn - Train an almost arbitrary scikit-learn classifier 1
qiime feature-table core-features - Identify core features in table 1
qiime feature-table filter-features - Filter features from table 1
qiime feature-table filter-samples - Filter samples from table 1
qiime feature-table filter-seqs - Filter features from sequences 1
qiime feature-table group - Group samples or features by a metadata column 1
qiime feature-table heatmap - Generate a heatmap representation of a feature table 1
qiime feature-table merge - Combine multiple tables 1
qiime feature-table merge-seqs - Combine collections of feature sequences 1
qiime feature-table merge-taxa - Combine collections of feature taxonomies 1
qiime feature-table presence-absence - Convert to presence/absence 1
qiime feature-table rarefy - Rarefy table 1
qiime feature-table relative-frequency - Convert to relative frequencies 1
qiime feature-table subsample - Subsample table 1
qiime feature-table summarize - Summarize table 1
qiime feature-table tabulate-seqs - View sequence associated with each feature 1
qiime gneiss add-pseudocount - Add pseudocount to table 1
qiime gneiss assign-ids - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns. 1
qiime gneiss balance-taxonomy - Balance Summary 1
qiime gneiss correlation-clustering - Hierarchical clustering using feature correlation. 1
qiime gneiss dendrogram-heatmap - Dendrogram heatmap. 1
qiime gneiss gradient-clustering - Hierarchical clustering using gradient information. 1
qiime gneiss ilr-transform - Isometric Log-ratio Transform 1
qiime gneiss lme-regression - Simplicial Linear mixed effects regression 1
qiime gneiss ols-regression - Simplicial Ordinary Least Squares Regression 1
qiime longitudinal first-differences - Compute first differences or difference from baseline between sequential states 1
qiime longitudinal first-distances - Compute first distances or distance from baseline between sequential states 1
qiime longitudinal linear-mixed-effects - Linear mixed effects modeling 1
qiime longitudinal nmit - Nonparametric microbial interdependence test 1
qiime longitudinal pairwise-differences - Paired difference testing and boxplots 1
qiime longitudinal pairwise-distances - Paired pairwise distance testing and boxplots 1
qiime longitudinal volatility - Volatility analysis 1
qiime metadata distance-matrix - Create a distance matrix from a numeric Metadata column 1
qiime metadata tabulate - Interactively explore Metadata in an HTML table 1
qiime phylogeny fasttree - Construct a phylogenetic tree with FastTree. 1
qiime phylogeny filter-table - Remove features from table if they're not present in tree. 1
qiime phylogeny midpoint-root - Midpoint root an unrooted phylogenetic tree. 1
qiime quality-control evaluate-composition - Evaluate expected vs. observed taxonomic composition of samples 1
qiime quality-control evaluate-seqs - Compare query (observed) vs. reference (expected) sequences. 1
qiime quality-control exclude-seqs - Exclude sequences by alignment 1
qiime quality-filter q-score - Quality filter based on sequence quality scores. 1
qiime quality-filter q-score-joined - Quality filter based on joined sequence quality scores. 1
qiime sample-classifier classify-samples - Supervised learning classifier. 1
qiime sample-classifier maturity-index - Microbial maturity index prediction. 1
qiime sample-classifier regress-samples - Supervised learning regressor. 1
qiime taxa barplot - Visualize taxonomy with an interactive bar plot 1
qiime taxa collapse - Collapse features by their taxonomy at the specified level 1
qiime taxa filter-seqs - Taxonomy-based feature sequence filter. 1
qiime taxa filter-table - Taxonomy-based feature table filter. 1
qiime tools export - Export data from a QIIME 2 Artifact or Visualization. 1
qiime tools export collection - Export data from a QIIME 2 Artifact or Visualization. 1
qiime tools export to paired collection - Export data from a QIIME 2 Artifact or Visualization. 1
qiime tools import - Import data into a new QIIME 2 Artifact. 1
qiime vsearch cluster-features-closed-reference - Closed-reference clustering of features. 1
qiime vsearch cluster-features-de-novo - De novo clustering of features. 1
qiime vsearch cluster-features-open-reference - Open-reference clustering of features. 1
qiime vsearch dereplicate-sequences - Dereplicate sequences. 1
qiime vsearch join-pairs - Join paired-end reads. 1
qiime vsearch uchime-denovo - De novo chimera filtering with vsearch. 1
qiime vsearch uchime-ref - Reference-based chimera filtering with vsearch. 1
QualityScoreDistribution chart quality score distribution 14
Quast Genome assembly Quality 14
Ramachandran Analysis - Ramachandran plot for proteins 2
Ramachandran Plots - calculate and plot the distribution of two dihedrals in a trajectory 4
Rarefaction.shared Generate inter-sample rarefaction curves for OTUs 5
Rarefaction.single Generate intra-sample rarefaction curves for OTUs 6
RDF Analysis - Radial Distribution Function between two atoms 4
Realigner Target Creator for use in local realignment 3
Recentrifuge Robust comparative analysis and contamination removal for metagenomics Statistical calculation Taxonomic classification 3
Reduce Reads in BAM files 3
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 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 sequences 5
Rename.seqs Rename sequences by concatenating the group name 2
ReorderSam reorder reads to match ordering in reference sequences 17
Replace parts of text 12
Replace Text in a specific column 11
Replace Text in entire line 11
ReplaceSamHeader replace header in a SAM/BAM dataset 17
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
RMSD Analysis using Bio3D 2
RMSF Analysis using Bio3D 2
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly Sequence alignment 19
Run a core set of QIIME diversity analyses (core_diversity_analyses) 2
Run join_paired_ends on multiple files (multiple_join_paired_ends) 2
Run split_libraries_fastq on multiple files (multiple_split_libraries_fastq) 2
sam-to-unsorted.bam converter 1
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 19
Samtools depth compute the depth at each position or region 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
Scatterplot of two numeric columns 4
Scatterplot with ggplot2 10
Screen.seqs Screen sequences 6
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Search in textfiles (grep) 11
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 Variants from VCF files 3
Send to cloud 1
Sens.spec Determine the quality of OTU assignment 6
Seq.error assess error rates in sequencing data 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
Sequence Splitter Data handling Splitting 2
SFF converter 1
Sffinfo Summarize the quality of sequences 5
Shhh.flows Denoise flowgrams (PyroNoise algorithm) 5
Shhh.seqs Denoise program (Quince SeqNoise) 5
Shovill Faster SPAdes assembly of Illumina reads 8
SICER Statistical approach for the Identification of ChIP-Enriched Regions 3
Slice MD trajectories using the MDTraj package 3
smi-to-mol converter 2
smi-to-smi converter 2
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL2 2
SMILES to SDF 2
snp location to bed format convert SNP to interval 1
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.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 fastq libraries to performs demultiplexing of Fastq sequence data (split_libraries_fastq) 2
Split libraries according to barcodes specified in mapping file (split_libraries) 2
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
sRNAPipe In-depth study of small RNA 4
STAR-Fusion detect fusion genes in RNA-Seq data 4
staramr Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes. 11
Stitch Gene blocks given a set of coding exon intervals 4
Stitch MAF blocks given a set of genomic intervals 1
Sub.sample Create a sub sample 5
Summarize taxa and store results in a new table or appended to an existing mapping file (summarize_taxa) 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
tabular-to-csv converter 1
tac reverse a file (reverse cat) 9
Tandem Repeats Finder locates and displays tandem repeats in DNA sequences 1
tar-to-directory converter 2
Taxonomy-to-Krona convert a mothur taxonomy file to Krona input format 2
Text reformatting with awk 13
Text transformation with sed 11
TopHat Gapped-read mapper for RNA-seq data 9
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
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 15
Trinity de novo assembly of RNA-Seq data 14
Unfold columns from a table 11
Unified Genotyper SNP and indel caller 3
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
Unipept retrieve taxonomy for peptides 6
Unique occurrences of each record 9
Unique lines assuming sorted input file 11
Unique.seqs Return unique sequences 5
unique_line remove duplicate lines 1
Upload File from your computer Query and retrieval 3
Validate Variants 3
ValidateSamFile assess validity of SAM/BAM dataset 15
Variant Annotator 3
Variant Filtration on VCF files 3
Variant Recalibrator 3
VCF to MAF Custom Track for display at UCSC 2
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
visualise pore diameter of AQP 1
WIG parser 1
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2