Référentiel des outils installés sur la plateforme Migale

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


SpoTyping (version 2.1 - 2019-02-06)
SpoTyping is a fast and accurate program for in silico spoligotyping of Mycobacterium tuberculosis isolates from next-generation sequencing reads.
Usage : #SpoTyping.py [options] FASTQ_1/FASTA FASTQ_2(optional)



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.



SurfG+ (version 1.02 - 2012-07-13)
SurfG+ is a tool to predict the protein localization in frame-psoitive bacteria. Current protein localization protocols are not suited to this prediction task as they ignore the potential surface exposition of many membrane-associated proteins. Therefore, we developed a new flow scheme, for the processing of protein sequence data with the particular aim of identification of potentially surface exposed (PSE) proteins from Gram-positive bacteria.
Remarque : See Barinov A, Loux V, Hammani A, Nicolas P, Langella P, Ehrlich D, et al. Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria.Proteomics. 2009 Jan.;9(1):61–73.  
Usage : #Surfg



tablet (version 1.14.10.20 - 2015-04-07)
Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.
Usage : #tablet



Tandem Repeats Finder (version 4.07b - 2013-08-20)
A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
Usage : #trf



T-Coffee (version 11.00.8cbe486 - 2015-04-07)
T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.
Usage : #t_coffee sequence_file


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by Dr. Radut