Référentiel des outils installés sur la plateforme Migale

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...

agmial (version - 2004-10-12)

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

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

bcftools (version 1.2 - 2015-04-15)
BCFs.bcftools (Tools for variant calling and manipulating VCFs and BCFs)
Usage : #bcftools

bedtools (version 2.16.2 - 2012-10-09)
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.
Remarque : Please cite the following article if you use BEDTools in your research: Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.

bfast (version 0.7.0 - 2013-08-12)
BFAST : Blat-like Fast Accurate Search Tool BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: * Speed: enables billions of short reads to be mapped quickly. * Accuracy: A priori probabilities for mapping reads with defined set of variants. * An easy way to measurably tune accuracy at the expense of speed.
Usage : #bfast [options]

bioprospector (version 2004 - 2014-01-01)
Usage : #BioProspector

bismark (version 0.14.3 - 2015-06-05)
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.
Usage : #bismark [options] {-1 -2 | }


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by Dr. Radut