| Version | MAJ | abyss | | |
| 1.5.2 | 2014-11-18 | Download | Doc |
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
Remarque | Run Unix # Usage: ABYSS [OPTION]... FILE... | Run Web # |
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.
Remarque Please cite the following article if you use BEDTools in your research:
Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
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The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service. The NCBI also distributes stand-alone BLAST applications for users who wish to run BLAST on their own machines or with their own databases. This document describes the stand-alone BLAST applications and will concentrate on the latest generation of such applications included in the BLAST+ package.
Remarque | Run Unix # /usr/local/genome/ncbi-blast-2.2.31+/bin/ | Run Web # |
| Version | MAJ | bowtie | | |
| 1.1.2 | 2016-07-24 | Download | Doc |
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
Remarque Run Unix # bowtie [options]* {-1 -2 | --12 | } [] | Run Web # |
BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence, except for disallowing gaps close to the end of the query. It can also be tuned to find a fraction of longer gaps at the cost of speed and of more false alignments.
Remarque | Run Unix # bwa [options] | Run Web # |
Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.
Remarque | Run Unix # cufflinks [options]* | Run Web # |
| Version | MAJ | cutadapt | | |
| 1.7.1 | 2015-03-11 | Download | Doc |
cutadapt is used to remove adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.
Remarque | Run Unix # cutadapt [options] [] | Run Web # |
SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.
Remarque
SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.
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FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
Remarque | Run Unix # fastqc ou fastqc seqfile1 seqfile2 .. seqfileN | Run Web # |
| Version | MAJ | Filter pileup | | |
| 1.0.2 | | Download | Doc |
Allows one to find sequence variants and/or sites covered by a specified number of reads with bases above a set quality threshold. The tool works on six and ten column pileup formats produced with samtools pileup command. However, it also allows you to specify columns in the input file manually.
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| Version | MAJ | FLASH | | |
| 1.2.11 | 2014-11-13 | Download | Doc |
FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool
to merge paired-end reads from fragments that are shorter than twice the
length of reads. The extended length of reads has a significant positive
impact on improvement of genome assemblies.
Remarque | Run Unix # flash [OPTIONS] MATES_1.FASTQ MATES_2.FASTQ
Run `flash --help | less' for more information. | Run Web # |
Find Rapidly OTUs with Galaxy Solution: FROGS is a galaxy/CLI workflow designed to produce an OTU count matrix from high depth sequencing amplicon data. This workflow is focused on: - User-friendliness with the integration in galaxy and lots of rich graphic outputs - Accuracy with a clustering without global similarity threshold, the management of multi-affiliations and management of separated PCRs in the chimera removal step - Speed with fast algorithms and an easy to use parallelisation - Scalability with algorithms designed to support the data growth
Remarque
HMMER: profile HMMs for protein sequence analysis Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
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| Version | MAJ | Illumina CASAVA-1.8 FASTQ Filter | | |
| 0.1 | 2014-04-30 | Download | Doc |
The recent version of Illumina's CASAVA pipeline (Version 1.8) produces FASTQ files with both reads that pass filtering and reads that don't.
The new READ-ID (the @ line) contains many new fields, one of them indicates whether the read is filtered or not.
This program can filter FASTQ files produced by CASAVA 1.8, and keep/discard reads based on this filter flag.
Remarque | Run Unix # fastq_illumina_filter -h | Run Web # |
| Version | MAJ | Klast | | |
| 4.4 | 2015-04-24 | Download | Doc |
KLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture, KLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.
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| Version | MAJ | LEfSe | | |
| 2014-12-24 | Download | Doc |
LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance. LEfSe is available as a Galaxy module, and as a bitbucket repository. For additional information, please refer to the LEfSe paper. We provide support for LEfSe users. Please join our Google group designated specifically for LEfSe users. F
Remarque
The goal of mothur is to have a single resource to analyze molecular data that is used by microbial ecologists. Many of these tools are available elsewhere as individual programs and as scripts, which tend to be slow or as web utilities, which limit your ability to analyze your data. mothur offers the ability to go from raw sequences to the generation of visualization tools to describe α and β diversity. Examples of each command are provided within their specific pages, but several users have provided several analysis examples, which use these commands. An exhaustive list of the commands found in mothur is available within the commands category index.
Remarque | Run Unix # mothur | Run Web # |
| Version | MAJ | prinseq | | |
| 0.17.1 | 2013-08-20 | Download | Doc |
PRINSEQ CAN BE USED TO FILTER, REFORMAT, OR TRIM YOUR GENOMIC AND METAGENOMIC SEQUENCE DATA. IT GENERATES SUMMARY STATISTICS OF YOUR $
GRAPHICAL AND TABULAR FORMAT.
Remarque | Run Unix # prinseq-lite.pl -h | Run Web # |
| Version | MAJ | prodigal
| | |
| 2.60 | 2013-03-26 | Download | Doc |
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include:
Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.
Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly).
Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%.
GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations.
Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.
Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.
Remarque Prodigal Reference: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11(1):119. (Highly Accessed) | Run Unix # prodigal -h
| Run Web # |
Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.
Remarque | Run Unix # prokka [options]
| Run Web # |
QIIME (pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to single studies based on billions of sequences from thousands of samples.
Remarque | Run Unix # qiime_env | Run Web # |
QUality ASsesment Tool for Genome Assembly
QUAST evaluates a quality of genome assemblies by computing various metrics and providing nice reports.
Remarque Citation : Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler,
QUAST: quality assessment tool for genome assemblies,
Bioinformatics (2013) 29 (8): 1072-1075.
doi: 10.1093/bioinformatics/btt086
First published online: February 19, 2013 | Run Unix # quast.py [options]
metaquast.py [options] | Run Web # |
Easy identification and removal of rRNA-like sequences.
The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
Remarque Run Unix # ribopicker [options] -f -dbs ... | Run Web # |
Programme pour détecter des mots ou motifs ayant une fréquence statistiquement exceptionnelle dans une séquence biologique. (R'MES pour Recherche de Mots Exceptionnels dans les Séquences)
Remarque Voici ce qu'il y a de nouveau par rapport à la version 3.01 : Changements majeurs : - amélioration significative du temps de calcul dans le cas des approximations Gaussiennes, quelque soit l'ordre du modèle, - levée de la contrainte sur la taille des noms des familles de mots. Changements mineurs : - renommage des options de sélection de seuil dans l'outil de mise en forme des résultats (--minthresh et --maxthresh deviennent --tmin et --tmax), - modification de l'ordre de présentation pour les résultats de calcul de biais (triés selon le score, et non plus alphabétiquement). Pour toutes questions, contactez Sophie.Schbath@jouy.inra.fr| Run Unix # rmes [options] -s -o rmes --help | Run Web # |
Remarque | Run Unix # rmesplot | Run Web # |
| Version | MAJ | samToFastq | | |
| 1.62(1113)
| 2012-02-17 | Download | Doc |
Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger fastq format. In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM file will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.
Remarque
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Remarque | Run Unix # samtools [options] | Run Web # |
| Version | MAJ | sickle | | |
| 1.200 | 2013-02-26 | Download | Doc |
sickle - A windowed adaptive trimming tool for FASTQ files using quality
Remarque | Run Unix # sickle [options] | Run Web # |
SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity.
Remarque If you use SortMeRNA, please cite:
Kopylova E., Noé L. and Touzet H., "SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611. | Run Unix # sortmerna -h
| Run Web # |
SPAdes is a de Bruijn graph based assembler. It integrates a read error corrector, a multiple kmer De Bruijn graph assembler, an assembly merger, a scaffoler and a repeat resolver.
Remarque | Run Unix # spades | Run Web # |
| Version | MAJ | SurfG+ | | |
| 1.02 | 2012-07-13 | Download | Doc |
SurfG+ is a tool to predict the protein localization in frame-psoitive bacteria. Current protein localization protocols are not suited to this prediction task as they ignore the potential surface exposition of many membrane-associated proteins. Therefore, we developed a new flow scheme, for the processing of protein sequence data with the particular aim of identification of potentially surface exposed (PSE) proteins from Gram-positive bacteria.
Remarque See Barinov A, Loux V, Hammani A, Nicolas P, Langella P, Ehrlich D, et al. Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria.
Proteomics. 2009 Jan.;9(1):61–73.
| Run Unix # Surfg | Run Web # |
| Version | MAJ | TMAP | | |
| 3.4.1 | 2013-10-25 | Download | Doc |
TMAP / Torrent Mapping Alignment Program - Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.
Remarque
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Remarque | Run Unix # tophat -h | Run Web # |
Trimmomatic: A flexible read trimming tool for Illumina NGS data
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Remarque | Run Unix # trimmomatic | Run Web # |
| Version | MAJ | Trinity | | |
| 2.2.0 | 2016-07-01 | Download | Doc |
RNA-Seq De novo Assembly Using Trinity
Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads.
Remarque | Run Unix # Trinity | Run Web # |
Sequence assembler for very short reads. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
Remarque | Run Unix # velveth # velvetg | Run Web # |
