Référentiel des outils installés sur la plateforme Migale

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


abyss (version 1.5.2 - 2014-11-18)
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.
Usage : #Usage: ABYSS [OPTION]... FILE...



Admixture (version 1.3 - 2019-02-12)
ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.
Usage : #admixture



agmial (version - 2004-10-12)



amos (version 3.1.0 - 2013-08-12)
AMOS: A Modular Open-Source Assembler



AnnotSV (version 1.1 - 2018-05-16)
Outilis permettant l'annotation de variant structuraux, peu d'outils existe en la matiere
Download : AnnotSV
Documentation : http://lbgi.fr/AnnotSV/



apollo (version 1.11.8 - 2013-08-11)
Apollo is a genomic annotation viewer and editor. There are currently two branches of Apollo, one primarily used for genome browsing and maintained at Ensembl, and the other primarily used for genome annotation and maintained at the Berkeley Drosophila Genome Center. The latter is part of the GMOD project.
Usage : #apollo



artemis (version 15.0 - 2013-08-07)
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
Usage : #art



bam2fastq (version 1.1.0 - 2019-07-31)
Convertisseur simple de fichiers BAM en fichiers FASTQ. Aide à la conversion de fichiers bam paired-end en fichiers fastq.
Usage : #bam2fastq [options]



bamaddrg (version - - 2019-03-27)
bamaddrg: adds read groups to input BAM files, streams BAM output on stdout. This is intended for use "fixing up" RG tags on the fly so that they reflect the source file from which the aligment originated from. This allows the "safe" merging of many files from many individuals into one stream, suitable for input into downstream processing systems such as freebayes (a population variant detector).
Usage : #bamaddrg [-b FILE [-s NAME [-r GROUP]]]



BamM (version 17.3 - 2018-11-08)
BamM is a c library, wrapped in python, that parses BAM files. The code is intended to provide a faster, more stable interface to parsing BAM files than PySam, but doesn't implement all/any of PySam's features. Do you want all the links that join two contigs in a BAM? Do you need to get coverage? Would you like to just work out the insert size and orientation of some mapped reads? Then BamM is for you!
Usage : #bamm_env


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by Dr. Radut