Référentiel des outils installés sur la plateforme Migale
La liste des packages R installés sur la plateforme Migale est disponible ici.
dadi (version 1.7 - 2016-07-18)
Download : https://bitbucket.org/gutenkunstlab/dadi
Remarque : If you use ???a???i in your research, please cite RN Gutenkunst, RD Hernandez, SH Williamson, CD Bustamante "Inferring the joint demographic history of multiple populations from multidimensional SNP data" PLoS Genetics 5:e1000695 (2009).
DART (version 1.2.4 - 2018-01-09)
DART: a fast and accurate RNA-seq mapper with a divide and conquer strategy
Download : https://github.com/hsinnan75/DART
Documentation : https://github.com/hsinnan75/DART
Usage : #dart -i Index_Prefix -f
debarcer (version 0.3.1 - 2017-03-21)
Debarcer (De-Barcoding and Error Correction) is a package for working withnext-gen sequencing data that contains molecular barcodes.As it stands, it supports targeted sequencing libraries generated bySimSenSeq, a method of creating multiplexed barcoded sequencing librariesusing PCR.
Download : https://github.com/oicr-gsi/debarcer
Usage : #runDebarcer.sh -u
delly (version 0.6.3 - 2015-02-25)
DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.
Remarque : CitationTobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M. Stuetz, Vladimir Benes, Jan O. Korbel.Delly: structural variant discovery by integrated paired-end and split-read analysis.Bioinformatics 2012 28: i333-i339.
Usage : #Usage: delly [OPTIONS]
diamond (version 0.7.9 - 2015-12-02)
DIAMOND is a new high-throughput program for aligning a file of short reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500 times faster than BLASTX, finding more than 94% of all matches.
Documentation : https://github.com/bbuchfink/diamond/blob/master/README.rst
Usage : #diamond COMMAND [OPTIONS]
diyabc (version 2.1.0 - 2018-02-02)
a user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers
Download : http://www1.montpellier.inra.fr/CBGP/diyabc/
Documentation : http://genome.jouy.inra.fr/doc/genome/Outils-calcul-num%C3%A9riques/diyabc-2.1.0-linux64/diyabc-2.1.0-UserManual.pdf
Usage : #diyabc
DOMIRE (version - - 2014-01-20)
(DOMain Identification from REcurrence) is a server using VAST (Vector Alignment Search Tool, protein 3D structure comparison) to define the domain boundaries in proteins from their 3 D structures (Tai et al, 2010). It provides also a list of structural neighbours.
EDGE-pro (version 1.3.1 - 2013-07-02)
EDGE-pro, Estimated Degree of Gene Expression in PROkaryots is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignment and then estimates expression directly from the alignment results.EDGE-pro includes routines to assign reads aligning to overlapping gene regions accurately. 15% or more of bacterial genes overlap other genes, making this a significant problem for bacterial RNA-seq, one that is generally ignored by programs designed for eukaryotic RNA-seq experiments.
Documentation : http://genome.jouy.inra.fr/doc/genome/NGS/EDGE-pro-1.3.1/
Remarque : Please reference our paper:T. Magoc, D. Wood, and S.L. Salzberg. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. Evolutionary Bioinformatics vol.9, pp.127-136, 2013.
Usage : #edge.pl <-g genome> <-p ptt> <-r rnt> <-u reads>
eggnog-mapper (version 0.99.3 - 2017-07-13)
eggnog-mapper is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
Documentation : https://github.com/jhcepas/eggnog-mapper/wiki
Remarque : Merci d'avance, cordialement
Usage : #emapper.py [-h]
emboss (version 18.104.22.168 - 2013-08-19)
Within EMBOSS you will find around 100 programs (applications). These are just some of the areas covered (Sequence alignment, Rapid database searching with sequence patterns,Protein motif identification, including domain analysis, Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats, Codon usage analysis for small genomes, Rapid identification of sequence patterns in large scale sequence sets, Presentation tools for publication...)
Download : http://emboss.sourceforge.net/download/