Référentiel des outils installés sur la plateforme Migale

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

BasicQC (version - - 2019-12-03)
Outil permettant la création d'un rapport qualité après un séquençage nanopore
Usage : #conda activate BasicQC

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

bedtools (version 2.27.1 - 2020-10-15)
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]

Bioconvert (version 0.1.2 - 2018-11-15)
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another. Merci Véro !

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 | }

bjhuil (version uy - 2018-05-21)
Download : uyouy
Documentation : uyuy
Remarque : yuiooooooooooooo
Usage : #oyuiiiiiiiii

blast (version 2.2.26 - 2012-03-07)
Usage : #blastall

blast+ (version 2.2.31 - 2015-08-24)
The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service. The NCBI also distributes stand-alone BLAST applications for users who wish to run BLAST on their own machines or with their own databases. This document describes the stand-alone BLAST applications and will concentrate on the latest generation of such applications included in the BLAST+ package.
Usage : #/usr/local/genome/ncbi-blast-2.2.31+/bin/


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by Dr. Radut