Référentiel des outils installés sur la plateforme Migale


Trimmomatic (version 0.32 - 2014-01-06)
Trimmomatic: A flexible read trimming tool for Illumina NGS dataTrimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Usage : #trimmomatic



uchime (version 4.2.40 - 2013-05-27)
UCHIME is an algorithm for detecting chimeric sequences.
Usage : #uchime --input query.fasta [--db db.fasta] [--uchimeout results.uchime] [--uchimealns results.alns]



uclust (version 1.2.22q - 2012-11-06)
UCLUST is a high-performance clustering, alignment and search algorithm that is capable of handling millions of sequences.
Usage : #uclust --sort seqs.fasta --output seqs_sorted.fasta



usearch (version 8.0.1517 - 2015-03-10)
USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
Usage : #usearch



VarScan (version 4.2.3 - 2017-02-16)
variant detection in massively parallel sequencing data???
Usage : #varscan [COMMAND] [OPTIONS]



Vcflib (version - 2017-03-10)
A C++ library for parsing and manipulating VCF files.



velvet (version 1.2.07 - 2013-08-07)
Sequence assembler for very short reads. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
Usage : #velveth # velvetg



weeder (version 1.4.2 - 2009-12-07)
Recherche nouveaux TFBSs dans un jeu de sequences fasta, recherche de plusieurs tailles et limite de mutations autorisees. Ne sort que les motifs ayant passe le tri stat, contrairement a MEME qui donne autant de motifs que specifie dans les parametres. Par defaut les stat de genome sont basees sur un promoteur de 1000 pb, mais possibilite d'utiliser des stats basees sur toute la sequence intergenique.
Remarque : Pavesi G, Mereghetti P, Mauri G, Pesole G. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res. 2004 32:W199-W203
Usage : #weederlauncher.out inputfilename speciescode analysistype



weederH (version 1.4.2 - 2009-12-07)
Recherche de TFBS et ECR dans des sequences homologues. Pas d'alignement necessaire en input, pas de prerequis de PWM. Mesure de la conservation relative entre les sequences par recherche d'oligo conserves et scoring de similarite globale entre deux sequences homologues. Permet de chercher aussi les enhancers distaux. Fonctionnerait sur des promoteurs non annotes (pas de TSS connu).
Remarque : Pavesi, G., Zambelli, F., Pesole, G. WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics 2007, 8:46
Usage : #weederH.out -f inputfilename -O speciescode



xplor-nih (version 2.30 - 2012-02-08)
X-PLOR is a program system for computational structural biology. X-PLOR stands for exploration of conformational space of macromolecules restrained to regions allowed by combinations of empirical energy functions and experimental data. But it also stands for exploration of modern concepts of structured programming in macromolecular simulation.
Usage : #xplor


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