Référentiel des outils installés sur la plateforme Migale

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

signalp (version 4.0 - 2014-05-07)
D?tection de s?quence signal et de site de clivage sur les s?quences prot?iques de bact?ries Gram+, Gram- et d'eucaryotes.
Remarque : The SIGNALP package is a property of Center for Biological Sequence Analysis It may be downloaded only by special agreement (contact software@cbs.dtu.dk).
Usage : #signalp

Snippy (version 3.2 - 2018-03-21)
Rapid bacterial SNP calling and core genome alignments
Usage : #snippy [options] --outdir --ref --pe1 --pe2

SortMeRNA (version 1.9 - 2014-02-20)
SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity.
Remarque : If you use SortMeRNA, please cite:Kopylova E., Noé L. and Touzet H., "SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611.
Usage : #sortmerna -h

SPAdes (version 3.11.1 - 2017-12-26)
SPAdes is a de Bruijn graph based assembler. It integrates a read error corrector, a multiple kmer De Bruijn graph assembler, an assembly merger, a scaffoler and a repeat resolver.
Usage : #spades

splitsTree (version 4.13.1 - 2014-06-23)
SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.
Usage : #SplitsTree

STAR (version 2.5 - 2017-10-26)
STAR (Spliced Transcripts Alignment to a Reference) is a fast NGS read aligner for RNA-seq data
Usage : #STAR [options]... --genomeDir REFERENCE --readFilesIn R1.fq R2.fq

StringTie (version 1.3.0 - 2016-09-07)
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-lengthtranscripts representing multiple splice variants for each gene locus. Itsinput can include not only the alignments of raw reads used by othertranscript assemblers, but also alignments longer sequences that have beenassembled from those reads.In order to identify differentially expressedgenes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).
Usage : #stringtie -h/--help

structure (version 2.3.4 - 2012-12-21)
The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
Usage : #structure

SUPER-FOCUS (version 0.26 - 2016-10-04)
SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agilehomology-based approach using a reduced SEED database to report thesubsystems present in metagenomic samples and profile their abundances. Thetool was tested with over 70 real metagenomes, and the results show that ourapproach accurately predicts the subsystems present in microbial communities,and it can be up to over 1,000 times faster than other tools.

surf (version 1.0 - 2006-01-31)
SeqUence Repository and Feature detectionsNucleotidic sequence production commonly involve several dedicated bioinformatic softwares for sequence basecalling, vector detection, etc.


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by Dr. Radut