Référentiel des outils installés sur la plateforme Migale

La liste des packages R installés sur la plateforme Migale est disponible ici.

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.
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.
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.
Usage : #cufflinks [options]*

dadi (version 1.7 - 2016-07-18)
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
Usage : #dart -i Index_Prefix -f [-f2 ]

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.
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 0.9.24 - 2019-12-03)
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.
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
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.


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