Référentiel des outils installés sur la plateforme Migale

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/

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 1.1.2 - 2016-07-24)
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

buster (version 2.10.3 <2016-12-07> - 2016-12-08)
BUSTER structure refinement package. Includes the refine program for running BUSTER refinement and loads of useful utilities.
Remarque : How to cite use of BUSTER :https://www.globalphasing.com/buster/wiki/index.cgi?BusterCite

bwa (version 0.7.12 - 2015-04-07)
BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence, except for disallowing gaps close to the end of the query. It can also be tuned to find a fraction of longer gaps at the cost of speed and of more false alignments.
Usage : #bwa [options]

canu (version 1.3 - 2016-10-18)
Canu is a fork of the Celera Assembler, designed for high-noisesingle-molecule sequencing (such as the PacBio RS II or Oxford NanoporeMinION).
Remarque : Citation: Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. bioRxiv. (2016).
Usage : #canu


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by Dr. Radut