Référentiel des outils installés sur la plateforme Migale
La liste des packages R installés sur la plateforme Migale est disponible ici.
cross_match (version 0.990329 - 2002-11-06)
Cross_Match uses the same algorithm as Swat but also allows the comparison of a pair of sequences to be constrained to bands of the Smith-Waterman matrix that surround one or more matching words in the sequences. This substantially increases speed for large-scale nucleotide sequence comparisons without compromising sensitivity.
Download : http://www.phrap.org/phredphrapconsed.html
Documentation : http://www.phrap.org/phredphrap/general.html
Usage : #cross_match
cufflinks (version 2.2.0 - 2014-05-06)
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.
Download : http://cufflinks.cbcb.umd.edu/downloads/
Documentation : http://cufflinks.cbcb.umd.edu/manual.html
Usage : #cufflinks [options]*
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>