Référentiel des outils installés sur la plateforme Migale
COLONY (version 188.8.131.52 - 2017-05-02)
COLONY is a Fortran program written by Jinliang Wang. It implements a maximum likelihood method to assign sibship and parentage jointly, using individual multilocus genotypes at a number of codominant or dominant marker loci.
Download : https://www.zsl.org/science/software/colony
consed (version 22.0 - 2014-04-30)
Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.
Documentation : http://bozeman.mbt.washington.edu/consed/consed.html
Remarque : Voir aussi autofinishs (http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11282977s)
Usage : #consed
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).
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]
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>