Référentiel des outils installés sur la plateforme Migale

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

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/

BLAST Parser (version 1.1.6. - 2018-04-17)
This is a Perl script for parsing BLAST output and converting it into a more compact form. The parser was tested with the default pairwise output format (-outfmt 0) of blastn, blastx and tblastx from BLAST+ 2.2.25 package, and should probably work with any other version.
Usage : #blast_parser.pl blastparsed.txt

blat (version 34 - 2008-01-11)
BLAT is a DNA/Protein Sequence Analysis program written by Jim Kent at UCSC. It is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 33 bases, and sometimes find them down to 22 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein blat on land vertebrates.
Usage : #blat

bowtie (version - 2017-11-06)
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
Usage : #bowtie --help


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