577 tool(s) found

Tool Description Topics Available version(s)
[SVDetect] BAM preprocessing to get abnormal pairs 1
[SVDetect] Compare structural variants between two samples 1
[SVDetect] Detect clusters of anomalously mapped pairs and identify structural variants Indel detection 1
aaChanges amino-acid changes caused by a set of SNPs 2
Add column to an existing dataset 3
Add metadata to a BIOM table Conversion Format validation 3
Add or Replace Groups 3
Aggregate datapoints Appends the average, min, max of datapoints per interval 2
alienTrimmer Fast trimming to filter out non-confident nucleotides and alien oligo-nucleotide sequences (adaptors, primers) in both 5' and 3' read ends 1
animalerie-wf Taxonomic classification 1
Annotate smRNA dataset by iterative alignments with sRbowtie Mapping Sequence annotation 3
AnnotateBed annotate coverage of features from multiple files 17
AnnotatePeaks Genomic annotation of Chip-Seq peaks 2
Annotation of genes with Chip-Seq peaks 1
Annovar annotate genetic variants detected from human genome 1
Annovar Annotate Variation annotate genetic variants detected from diverse genomes 1
Apply Variant Recalibration 3
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment Conversion 1
AXT to FASTA Converts an AXT formatted file to FASTA format Conversion 1
AXT to LAV Converts an AXT formatted file to LAV format Conversion 1
BAM Index Statistics 3
BAM to BED converter 19
BAM to BigWig Calculates coverage from a BAM alignment file 3
BAM to SAM converts a list of BAM format files to SAM format 1
BAM-to-SAM convert BAM to SAM 7
Bam2Fastq extract reads from a bam file and write them in fastq format 1
Bam2roi Create ROI from BAM file. 1
bamCoverage generates a coverage bigWig file from a given BAM file 17
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 2
Base Coverage of all intervals Quantification 5
Base Recalibrator calculates covariates used to recalibrate base quality scores of reads 3
BCF Tools Cat This tool allows the user to concatenate BCF files. 2
BCF Tools Index This tool allows the user to index sorted BCF for random access. 2
bcftools view Converts BCF format to VCF format 11
BEAM significant single- and multi-locus SNP associations in case-control studies 1
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
bigWigToBedGraph Convert from bigWig to bedGraph format 3
biomarker_discovery_wf Taxonomic classification 1
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
Blast-Besthits filter Select the best hit for each query sequence in a Blast tabular file 1
Blast-hits filter for each line in a Blast file 1
blast_best_score Returns the list best hits from a list of BLAST results. 1
blast_to_scaffold Generate DNA scaffold from blastn or tblastx alignment of Contigs Scaffolding 2
BMGE cleaning aligned sequences Sequence alignment refinement 2
Booster Compute BOOSTER bootstrap supports 2
Bowtie2 - map reads against reference genome 21
Boxplot of quality statistics 2
breseq find mutations in haploid microbial genomes DNA mapping Genetic mapping Genome annotation Mapping assembly Protein SNP mapping Sequence word comparison 2
Breseq BAM2ALN - v0.26 1
Breseq BAM2COV - v0.26 Create a coverage plot or table for the specified region 1
cap3 Sequence Assembly tool DNA mapping Mapping Mapping assembly Sequence assembly 2
CapsuleFinder Program that detects capsule systems with high accuracy in proteic sequences. It is based on the program MacsyFinder which uses HMM profiles for the detection of the essential proteins of capsule biogenesis. Coding region prediction 1
Cas_finder Detection and classification of Cas (CRISPR-associated) proteins using MacSyFinder. Coding region prediction 1
CD-HIT Cluster a nucleotide dataset into representative sequences 1
CEAS Annotate intervals and scores with genome features 3
Change Case of selected columns 1
change gff Features Changes one feature name by an other name (the feature name can be found on the 3rd column). 1
change tag name Changes the name of tag of a list of transcripts. 1
changeName Change the chromosome name or gene name of a singla fasta, gff or sam file. For this tool, it can not treat mutiple-chromosome, gene files. 1
Chao / Simpson / Shannon Compute Chao, Simpson and Shannon values from Sabund and Rabund files 1
ChIPmunk - de novo motif finding 1
Circos visualizes data in a circular layout 6
Clean NGS Use adapters definition file ADAPTER.txt and remove the adapters from the input read files. The program writes out the cleansed reads and the rejected reads. Nucleotides are also removed based on quality thresholds from the 5' and 3'. 1
Clean Transcript File Clean a transcript file so that it is useable for S-MART. 1
Clip adapter sequences 5
Clip adapter Nucleic acid feature detection Nucleic acid sequence comparison Sequence feature detection Sequence motif comparison Sequence motif discovery 2
ClosestBed find the closest, potentially non-overlapping interval 17
Clustal Omega Multiple sequence alignment software Multiple sequence alignment Tree-based sequence alignment 2
ClustalW multiple sequence alignment program for DNA or proteins 4
Cluster the intervals of a dataset Sequence clustering Sequence merging 5
Clustering summary create a clustering summary tab for cd-hit and CROP. 1
Clusterize Clusterizes the reads when their genomic intervals overlap. 1
clusterize By SlidingWindows Produces a GFF3 file that clusters a list of transcripts using a sliding window. Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks. 1
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
CodonW Correspondence Analysis of Codon Usage. Sequence composition calculation 1
Collapse sequences 3
collapse reads Merges two reads if they have exactly the same genomic coordinates. 1
colorGff Parses a DOOR report file and writes the information in a gff3 out file. 1
Column Regex Find And Replace 3
Combine Variants 3
Compare Overlapping Print all the transcripts from a first file which overlap with the transcripts from a second file. 1
Compare Overlapping Small Query Provide the queries that overlap with a reference, when the query is small. 1
Compare Overlapping Small Reference Provide the queries that overlap with a reference, when the reference is small. 1
Compare taxonomy summary for several taxonomy summary files 1
Compare two Datasets to find common or distinct rows 1
CompareOverlapping_parallel Shrink or extend the sets of genomic coordinates to get the information between starts of reads and starts of genes. 1
Complement intervals of a dataset Sequence coordinate conversion 4
Compute coverage Compute the coverage of a set with respect to another set. 1
Compute quality statistics 3
Compute quality statistics for SOLiD data 1
Concatenate two datasets into one dataset Aggregation 5
Concatenate datacollection tail-to-head 1
Concatenate datasets tail-to-head 1
ConjScan : MacSyFinder-based detection of Conjugative elements using systems modelling and similarity search Coding region prediction 1
Consensus from VCF and Fasta Apply VCF variants to a fasta file to create a new consensus sequence. 1
Convert delimiters to TAB 1
Convert SOLiD output to fastq 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 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 FindPeaks output (.peaks) into Bed 1
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 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 BAM without sorting 1
Convert tabular to dbnsfp 2
Convert transcript file Convert a file from a format to another. 1
Convert uncompressed BCF to BCF 1
Convert2Annovar Convert other genotype calling format into ANNOVAR format 1
coordinates to sequence Coordinates to Sequences: Extract the sequences from a list of coordinates. 1
Count occurrences of each record 2
Count intervals in one file overlapping intervals in another file 2
count read GCpercent Count GC percent for each read against a genome. 1
countNumber Calculate the number of reads(annotations) overlapping for each transcript. 1
countNumber_parallel Calculate the number of reads(annotations) overlapping for each transcript. 1
COV2HTML Convert Mapping to a simple Visualization and Analysis tools for RNA-Seq data (Prokaryote) Formatting 1
Coverage of a set of intervals on second set of intervals Comparison Filtering 5
coverage Gff Computes reads coverage form a "nbElements" tag and writes the calculated coverage in a gff3 out file. 1
Create a BedGraph of genome coverage 3
Create a histogram of genome coverage 3
Create single interval as a new dataset 1
CROP a clustering tool designed mainly for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU). 1
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
Cut columns from a table 2
Cutadapt Remove adapter sequences from Fastq/Fasta 16
Data Fetch 1
DAVID functional annotation for a list of genes 1
Decompress an archive in zip, gz, tar.gz, fastq.gz, fastq.bz2 or tar.bz2 format 2
Delta-Filter Filters alignment (delta) file from nucmer Read mapping Sequence alignment 3
Depth of Coverage on BAM files 3
DESEQ for differential expression analysis Differential expression analysis for reads count data 2
DESeq2 Determines differentially expressed features from count tables Differential gene expression analysis 18
Diamond generate formatted output from DAA files Sequence alignment analysis 3
Diamond alignment tool for short sequences against a protein database Sequence alignment analysis 7
Diamond makedb Build database from a FASTA file Sequence alignment analysis 7
DNAdiff Evaluate similarities/differences between two sequences Read mapping Sequence alignment 3
Draw nucleotides distribution chart 4
Draw quality score boxplot for SOLiD data 1
dsrc DNA Sequence Reads Compressor 1
DummyPasteur columns from a table 1
elp Computes synonymous sequences that maximize protein evolutionary landscape exploration Protein sequence feature detection Protein structural motif recognition Sequence motif recognition 1
Estimate Library Complexity 3
Eval Variants 3
export data for SynBioWatch To export history data for SynBioWatch projet files and user, WARNING this tool duplicate the data, remember to delete redundant data 1
export one data To export ONE history data, WARNING this tool duplicate the data, remember to delete redundant data 1
eXpress Quantify the abundances of a set of target sequences from sampled subsequences 2
Extract central region for a bed file 1
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 Pairwise MAF blocks given a set of genomic intervals 1
extract_fasta Extract fasta sequence Sequence conversion 1
extract_result Resume masque process Text annotation 1
fasta - tabular conversions Sequence conversion 2
Fasta Sequence Length Add length of sequence to fasta header 1
Fasta to Phylip Convert fasta alignment file into phylip interleaved format with goalign Formatting 1
Fasta to Phylip Convert fasta alignment file into phylip sequential format with goAlign Formatting 1
fastacmd : retrieves FASTA formatted sequences from a blast database Coding region prediction 1
fastaFromBed 1
FastME Distance-based inference of phylogenetic trees Phylogenetic tree analysis Phylogenetic tree generation (from molecular sequences) 4
Fastq -> Fasta Convert Fastq File to Fasta File. 1
FASTQ Groomer parallel convert between various FASTQ quality formats for a list of inputs 1
FASTQ interlacer on paired end reads Aggregation 6
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 5
fastq2fasta Convert fastq to fasta Sequence conversion 1
fastq2fasta2 Convert fastq to fasta Sequence conversion 1
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 19
FastQC for long read reports from FastQC with option for long reads 1
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
Fetch taxonomic representation 2
File motif counter Count or select lines containing a motif of a dataset 1
Filter data on any column using simple expressions Formatting 1
Filter bam file using mpileup and the bcf tools on coverage and SNPs and output a vcf file 1
Filter by quality Filtering 5
Filter FindPeaks output (.peaks) using Control Peaks 1
Filter GTF data by attribute values_list 1
Filter MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
Filter SAM or BAM files on FLAG MAPQ RG LN or by region Filtering Nucleic acid sequence analysis 3
Filter sequences by length Filtering 7
FIMO - Find Individual Motif Occurrences 11
FindPeaks a Peak Finder/Analysis application for the ChIP-Seq 1
findpromoter program to search for a promoter motif and optionally, an adapter sequence from a source species on a target species 1
Formatdb on fasta file Create a blast database using a fasta file 2
fqCleaner Mini workflow for preprocessing fastq files, it includes quality trimming, duplicate and artefacts filters for FASTQ read files 1
fqconvert Convert quality scoring to Sanger in FASTQ files 1
fqduplicate Detect duplicate reads. Outputs a list of read names corresponding to reads already seen in the dataset with a better quality sum score (duplicates) Repeat sequence analysis Sequence editing 1
fqextract: Pasteur fastq read extractor Extract a subset of fastq reads Sequence editing 1
fqquality Output reads with low quality bases trimmed (at the extremities) or masked and/or with quality descreased to the minimum. Output an extra singlet dataset if paired-end data provided. Sequence editing 1
fqseqname "List names of sequences from FASTQ formatted files" Sequence editing 1
fqseqpair "List names of sequence pairs from two FASTQ formatted files" Sequence motif analysis 1
FragGeneScan Application for finding (fragmented) genes in short and Error-prone Reads. Coding region prediction 1
FROGS Abundance normalisation Normalize OTUs abundance. Standardisation and normalisation 4
FROGS Affiliation OTU Taxonomic affiliation of each OTU's seed by RDPtools and BLAST Taxonomic classification 4
FROGS Affiliation postprocess Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics Taxonomic classification 2
FROGS Affiliations stat Process some metrics on taxonomies. Taxonomic classification 4
FROGS BIOM to std BIOM Converts a FROGS BIOM in fully compatible BIOM. Formatting 4
FROGS BIOM to TSV Converts a BIOM file in TSV file. Formatting 4
FROGS Clustering swarm Single-linkage clustering on sequences Taxonomic classification 4
FROGS Clusters stat Process some metrics on clusters. Clustering 4
FROGS Demultiplex reads Attribute reads to samples in function of inner barcode. Classification 4
FROGS Filters Filters OTUs on several criteria. Taxonomic classification 4
FROGS ITSx Extract the highly variable ITS1 and ITS2 subregions from ITS sequences. Sequence trimming 2
FROGS Pre-process merging, denoising and dereplication. Filtering 4
FROGS Remove chimera Remove PCR chimera in each sample. Editing 4
FROGS Tree Reconstruction of phylogenetic tree Taxonomic classification 2
FROGS TSV_to_BIOM Converts a TSV file in a BIOM file. Formatting 3
FROGS Upload archive from your computer 1
FROGSSTAT Phyloseq Alpha Diversity with richness plot Taxonomic classification 2
FROGSSTAT Phyloseq Beta Diversity distance matrix Taxonomic classification 2
FROGSSTAT Phyloseq Composition Visualisation with bar plot and composition plot Taxonomic classification 2
FROGSSTAT Phyloseq Import Data from 3 files: biomfile, samplefile, treefile Taxonomic classification 2
FROGSSTAT Phyloseq Multivariate Analysis Of Variance perform Multivariate Analysis of Variance (MANOVA) Taxonomic classification 2
FROGSSTAT Phyloseq Sample Clustering of samples using different linkage methods Taxonomic classification 2
FROGSSTAT Phyloseq Structure Visualisation with heatmap plot and ordination plot Taxonomic classification 2
g:Profiler tools for functional profiling of gene lists 1
GATK tool collection Version 3.6-0 1
gblocks Convert Aligned FASTA to phylip Extended Sequence masking 2
gdtools APPLY - v0.26 1
gdtools CHECK - v0.26 1
gdtools COMPARE/ANNOTATE - v0.26 Merge multiple GenomeDiff input files 1
gdtools GD2GVF - v0.26 1
gdtools GD2VCF - v0.26 1
gdtools INTERSECT - v0.26 1
gdtools MASK - v0.26 1
gdtools MUTATIONS - v0.26 1
gdtools NORMALIZE - v0.26 1
gdtools NOT-EVIDENCE - v0.26 1
gdtools SIMULATE-MUTATIONS - v0.26 1
gdtools SUBTRACT - v0.26 1
gdtools UNION - v0.26 1
gdtools VALIDATE 0.26 1
gdtools VCF2GD - v0.26 1
GemErr generate an error models from real data for GemReads 1
GemReads simulate Illumina and 454 reads 1
Genbank to fasta Automatically convert a GenBank-format file into FASTA format 1
Genbank to gene fasta Convert a Genbank file into the .ffn (gene) file 1
Genbank/EMBL protein/gene convertor Convert a Genbank/EMBL file into the .ffn (gene) file, .faa (protein fasta file) and ptt file (protein table), or sequin file 1
Genbank/EMBL/UniProt to GFF converter 1
Gene BED To Exon/Intron/Codon BED expander 1
Generate readmap and histograms from alignment files from sRbowtie aligment Map drawing Sequence visualisation 1
get Difference Gets all the regions of the genome, except the one given or get all the elements from the first set which does not ovelap with the second set (at the nucleotide level). 1
get differential expression Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file. 1
get distance Give the distances between every data from the first input set and the data from the second input set 1
get distribution Get Distribution: Get the distribution of the genomic coordinates on a genome. 1
get exons Get the exons of a set of transcripts. 1
Get Fasta from BioMAJ gets fasta genome corresponding to built-in indexes Data retrieval 1
get flanking Get the flanking regions of a set of reference. 1
Get flanks returns flanking region/s for every gene Sequence analysis 5
get introns Get the introns of a set of transcripts. 1
Get Letter Distribution Calculate distribution for each nucleotide per position for all short reads (S-MART) 1
get number Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster. 1
Get overlapping reads extracts reads with overlap signatures Nucleic acid sequence analysis 2
Get peak height distribution 1
get read distribution Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented. 1
get sequence Get a single sequence in a FASTA file. 1
get sizes Get the sizes of a set of genomic coordinates. 1
Get Subset for ChIP Control 1
get wig data Compute the average data for some genomic coordinates using WIG files 1
get wig distance Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome). 1
get wig profile Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome). 1
get_taxonomy Extract hit taxonomical annotation for target metagenomics databases Text annotation 1
GFF-to-BED converter Conversion 1
GMAP Genomic Mapping and Alignment Program for mRNA and EST sequences 2
GMAP Build a database genome index for GMAP and GSNAP 2
GMAP IIT Create a map store for known genes or SNPs 2
GMAP SNP Index build index files for known SNPs 2
GPASS significant single-SNP associations in case-control studies 1
Group data by a column and perform aggregate operation on other columns. 5
Growthpred predicts bacterial minimal doubling times by analysing codon usage bias in genomes and metagenomes. Codon usage analysis Codon usage table comparison Codon usage table formatting Gene regulatory network prediction Genetic code prediction 1
GSNAP Genomic Short-read Nucleotide Alignment Program 2
GTF-to-BEDGraph converter Conversion 1
html4blast Create a html report from a blast result Sequence editing 1
htseqCount This script takes an alignment file in SAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it 1
IgBlast Run IgBlast on data sequences to analyze Ig or TCR sequences. Database search 1
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Indel Realigner - perform local realignment 3
Insertion size metrics for PAIRED data 3
Integron Finder is a program that detects integrons in DNA sequences. Genome annotation Nucleic acid sequence feature detection Protein sequence feature detection Sequence motif recognition 1
interElementGff Creates a new Gff output, which corresponds to the region of two successive Elements. 1
Intersect Generate the intersection of two VCF files 2
Intersect the intervals of two datasets Filtering 5
Intersect BAM alignments with intervals in another files 2
Intersect intervals find overlapping intervals in various ways 17
intersectBed report overlaps between two feature files 1
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
khmer: Normalize By Median Filter reads using digital normalization via k-mer abundances Sequence file editing Sequence word comparison 4
Krona pie chart from taxonomic profile 9
kronaExtract kronaextract extracts from krona xml file (obtained by rankoptimizer), list of reads and blast offset for a given taxonomic name. 1
LAJ Pairwise Alignment Viewer 1
LAV to BED Converts a LAV formatted file to BED format 1
LD linkage disequilibrium and tag SNPs 1
Line/Word/Character count of a dataset 1
list annotation Shows the information of Annotation file -> Number of genes, rRNA, tRNA. 1
listInputs Give a list of input files from different conditions/groups for DESeq analysis, DESeq can then charge these input files from the given list. 1
load_multiFASTQfiles To load several FASTQ files from different conditions. 1
Lowest common ancestor finder Find the lowest common ancestor from a BLAST tabular file 1
LPS LASSO-Patternsearch algorithm 1
MACS Model-based Analysis of ChIP-Seq 2
MACS14 Model-based Analysis of ChIP-Seq (1.4.2) 3
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
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 Sequence Alignment 3
MakeTSSdist Get peak distribution around TSS 2
Map with Bowtie for Illumina 7
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 the pileup pipeline of ssaha2 for Illumina data 1
mapper analyzer Read the output of an aligner, print statistics and possibly translate into BED or GBrowse formats. 1
mappinghsp4taxo Analyses taxoptimizer output file to find the most relevant database's sequence using taxonomics informations (kronaextract output) and draw picture(s) with the mapping of all hsp on it. 1
Mark Duplicate reads 3
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
MEME - Multiple Em for Motif Elicitation 10
Merge the overlapping intervals of a dataset Sequence merging 4
Merge BAM Files merges BAM files together 3
Merge BedGraph files 3
Merge Columns together 2
merge sliding windows clusters Merges two files containing the results of a sliding windows clustering. 1
merge transcript lists Merge the elements of two lists of genomic coordinates. 1
metaSPAdes assembler for metagenomics datasets 3
MicroPITA Run Selects samples from abundance tables based on various selection schemes. 3
Mix Multi-Fasta for each sequence in a multi-fasta file 1
modify genomic coordinates Extend or shrink a list of genomic coordinates. 1
modify sequence list Extend or shring a list of sequences. 1
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
mpileup multi-way pileup of variants Sequence alignment visualisation 2
Mpileup convertor Convert a .mpileup file into a SynTView .coverage file 1
MrBayes with options and commands 2
Multifasta sequence(s) extractor Extract/Exclude one or more sequence(s) from a multifasta file using a dataset of identifiers. 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 Align two or more sequences Read mapping Sequence alignment 3
Mummerplot Generate 2-D dotplot of aligned sequences Read mapping Sequence alignment 3
Muscle Multiple sequence alignment Multiple sequence alignment 3
MutSpec Annot Annotate variants with ANNOVAR and other databases 2
MutSpec Compare Compare signatures with the cosine similarity method 2
MutSpec Filter Filter out variants present in public databases 2
MutSpec HotSpot Compute variant frequency on a defined dataset 1
MutSpec NMF Extract mutation signatures with the Non negative Matrix Factorization algorithm 2
MutSpec Split Split a tabular file by sample ID 2
MutSpec Stat Calculate various statistics on mutations 2
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
Newick Display Display a phylogenetic tree as SVG Phylogenetic tree visualisation 3
Noisy Cleaning aligned sequences Sequence masking 1
Nucmer Align two or more sequences Read mapping Sequence alignment 3
Oases_optimiser Auto optimise de novo RNA-seq Oases/Velvet assembly De-novo assembly DNA mapping Mapping Mapping assembly Sequence assembly 2
Paired Read Mate Fixer for paired data 3
Parallel Map with BWA for Illumina - map short reads (< 100 bp) against reference genome (mpi version) DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 2
Parse blast output and compile hits for virus discovery Sequence analysis 2
PASS significant transcription factor binding sites from ChIP data 1
Paste two files side by side 1
Pasteur blastall for NGS data Search nucleotide database with nucleotide query sequence(s) 1
PCM Taxonomic classification 1
pe filter split sorted fasta sequences Paired End into two seperate fasta files 1
Pear Paired-End read merger 4
PhageTerm Determine Bacteriophage Termini and Packaging Mode using randomly fragmented NGS data. Read mapping 2
phyloP interspecies conservation scores 1
PhyML Phylogeny software based on the maximum-likelihood Phylogenetic tree analysis Phylogenetic tree generation (from molecular sequences) 5
PhyML-SMS Maximum likelihood-based inference of phylogenetic trees with Smart Model Selection Phylogenetic tree analysis Phylogenetic tree generation (from molecular sequences) 3
Pick Fasta sequences with header satisfying a query string Filtering 2
Pileup to VCF Converts a pileup to VCF with filtering 2
Pindel Indel detection 3
Pindel2Vcf convert Pindel to VCF and index Conversion 2
plasmidspades genome assembler for plasmids 2
Plot Plot some information from a list of transcripts. 1
plot coverage Plot the coverage of the first data with respect to the second one. 1
plot genome coverage Get the coverage of a genome. 1
plotFingerprint plots profiles of BAM files; useful for assessing ChIP signal strength 17
prepare annotation file Prepares Annotation file -> clusterizes, filters exon and sorts annotations. 1
Preprocess files for SARTools generate design/target file and archive for SARTools inputs 5
Print Reads on BAM files 3
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 8
qual -> Fastq Convert a file in FASTA/Qual format to FastQ format. 1
Quality-aware fastq demultiplexer This program demultiplexes fastq data having "in-line" barcodes, based on a given list of barcodes and a barcode start position. It tries to assign each fastq record to the most likely barcode, taking into account the sequence qualities (interpreted as being Sanger-encoded). Filtering Splitting 1
rankoptimizer rankoptimizer report taxonomic abundance, based on BLAST hits. rankoptimizer analyze only (p)taxoptimizer output file. 1
RDP classify one or multiple samples 1
Read Fasta File This tool is the fastest and most efficient fasta-formatted sequence file (alphanumerical) sorting tool I have up front 1
Realigner Target Creator for use in local realignment 3
Reduce Reads in BAM files 3
reformat_fastq Reformats an input file generated by a MiSeq/HiSeq system, where reads are formatted in a scheme that includes a space-character, which might not correctly be used in downstream operations. 1
Remove beginning of a file 1
remove exon lines Removes the lines containing Exon. 1
Remove sequencing artifacts 5
Rename sequences 5
rename_fasta Rename fasta sequence Sequence conversion 1
ReorderSam reorder reads to match ordering in reference sequences 15
Replace strings in a text dataset 2
ReplaceSamHeader replace header in a SAM/BAM dataset 15
restrict from size Select the elements of a list of sequences or transcripts with a given size. 1
Restrict mpileup output to variants 1
restrict sequence list Keep the elements of a list of sequences whose name is mentionned in a given file. 1
restrict transcript list Keep the coordinates which are located in a given position. 1
Retrieve FASTA from NCBI Data retrieval 2
Reverse Complement a MAF file 1
Reverse-Complement 5
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly 13
rnaSPAdes assembler for RNA-Seq data 3
ROI Filter Filter ROI files 1
ROI Metrics Computation Compute metrics for records in an ROI file. 1
ROI Overview Report ROI Overview Report 1
ROI PCA Computation Compute PCA-based metric for records in an ROI file. 1
ROI Sorting Sort ROI file 1
ROI Table ROI Overview Report 1
ROI Thumbnail Plots Create ROI thumbnail plot grids. 1
RoiFeatureProjection Region Of Interest Projection. 1
Sabund and Rabund Make Sabund and Rabund files from a CD-HIT cluster output 1
Salmonella CRISPR Typing identify known spacers and DRs for Salmonella. Nucleic acid sequence analysis Sequence motif recognition 1
SAM-to-BAM convert SAM to BAM 11
SAM/BAM Alignment Summary Metrics 3
SAM/BAM GC Bias Metrics 3
SAM/BAM Hybrid Selection Metrics for targeted resequencing data 3
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 17
Samtools flagstat tabulate descriptive stats for BAM datset 8
Samtools idxstats reports stats of the BAM index file 8
Samtools sort order of storing aligned sequences 7
SARTools DESeq2 Compare two or more biological conditions in a RNA-Seq framework with DESeq2 6
SARTools edgeR Compare two or more biological conditions in a RNA-Seq framework with edgeR 5
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Search ENA data given a query 2
Secure Hash / Message Digest on a dataset 2
seedGff Creates the seed from -15 to -25 bp before ATG 1
Select lines that match an expression 1
select by tag Keeps the genomic coordinates such that a value of a given tag. 1
Select first lines from a dataset 1
Select last lines from a dataset 1
Select random lines from a file 2
Select Variants from VCF files 3
Sequence Splitter Data handling Splitting 1
Sequence type detection Detect sequence datatype on fasta file 1
setuppromoter builds a fasta file of sequences from a reference genome using promoter region coordinates. 1
SFF converter 1
Show-Coords Parse delta file and report coordinates and other information Read mapping Sequence alignment 3
Show-Tiling Parse delta file and report predicted location of each aligning query contig as mapped to the reference sequences. Read mapping Sequence alignment 1
SIFT predictions of functional sites 1
Simulate Illumina runs 1
Slice BAM by genomic regions 5
SlopBed adjust the size of intervals 18
Small RNA Signatures computes small RNA (piRNA, siRNA, ...) signatures Nucleic acid sequence analysis 3
small_rna_maps generates small read maps from alignment BAM files Map drawing RNA-seq read count analysis 4
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
snp/indel convertor Convert a tabular snpEff file into a SynTView .snp and .indel files 1
SnpEff eff: annotate variants 14
snpEff2 SNP effect for each SNP in a file 2
snpEff3 detects SNPs effect on transcripts. Compatible with Genbank files 1
snpEff4 detects SNPs effect on transcripts. Compatible with Genbank files 1
Sort data in ascending or descending order 2
sortGff Sorts a gff file. 1
SPAdes genome assembler for regular and single-cell projects Genome assembly 11
Split MAF blocks by Species 1
sR_bowtie for small RNA short reads DNA mapping Mapping Mapping assembly Sequence assembly 2
Stampy genome indexer Stampy genome indexer for divergent genomes 1
Stampy mapper Mapper for divergent genomes 1
Statistics on bam file Generate mapping statistics from the bam file 1
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
strictly include Gff Prints the elements which are strictly included in the template. 1
Subtract the intervals of two datasets Filtering 5
Summary Statistics for any numerical column 3
Taxonomy summary Count the redundancy from a taxonomy file 1
taxoptimizer Retrieves taxonomy using tabulate blast results 1
TNT phylogenetic analysis under parsimony 2
TopHat Gapped-read mapper for RNA-seq data 10
TopHat for Illumina Find splice junctions using RNA-seq data 3
Tophat parallel for Illumina Find splice junctions using RNA-seq data, can have several input RNA-seq data. 1
Trim leading or trailing characters 1
trim adaptors Remove the 3' adaptor of a list of reads. 1
Trim sequences 5
trim sequences Remove the 5' and/or 3' adaptors of a list of reads. 1
trimAl trimAl: a tool for automated alignment trimming Sequence masking 1
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 14
Trinity De novo assembly of RNA-Seq data Using Trinity EST assembly 2
TXSScan MacSyFinder-based detection of protein secretion systems and related appendages using systems modelling and similarity search. Coding region prediction 1
Unified Genotyper SNP and indel caller 3
Upload File from your computer 2
Validate Variants 1
Variant Annotator 3
Variant Filtration on VCF files 3
Variant Recalibrator 3
VCF substraction : substract one or more vcf file(s) from a first one 1
VCF to MAF Custom Track for display at UCSC 2
vcf-annotate Remove filtered lines from vcf files 1
vcfutils Program from SAMtools/BCFtools package (only vcf2fq command is implemented) 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
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
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2
writeResToHTML Write all ncRNAs analysis results into an HTML file (Only for ncRNAs analysis pipeline). 1
xxr Integrons Analysis and Cassette Identification Gene component prediction Gene prediction Gene regulatory network prediction Genetic code prediction 1