Référentiel des outils installés sur la plateforme Migale

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

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

bowtie2 (version 2.2.5 - 2015-04-07)
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
Usage : #bowtie2 [options]* -x {-1 -2 | -U } [-S ]

breakdancer (version 1.4.5 - 2015-03-06)
BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.
Usage : #Usage: breakdancer-max

bsmap (version 2.90 - 2015-03-17)
BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.
Remarque : Citation: Xi Y, Li W: BSMAP: whole genome Bisulfite Sequence MAPping program. BMC Bioinformatics (2009) 10:232.
Usage : #bsmap


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