Arrêt de l'ensemble des services de la plateforme Migale à partir du lundi 3 avril 2017

La plateforme Migale sera indisponible du 3 au 10 avril 2017. Cette indisponibilité est dûe à l'arrêt du DataCenter Ile-de-France qui héberge l'infrastructure de la plateforme.

Merci d'avance de votre compréhension.

Pour toutes questions ou informations supplémentaires, merci de contacter help.migale@jouy.inra.fr.

Analyse de variants


VersionMAJ

gatk

3.52016-01-25DownloadDoc
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

Remarque
Run Unix # java -jar /usr/local/genome/gatk/GenomeAnalysisTK.jar -hRun Web #

VersionMAJ

gril

1.0.0DownloadDoc
GRIL is a tool to detect the locations of genomic rearrangements in a set of sequences.

Remarque
Run Unix # grilRun Web #

VersionMAJ

novosnp

2.0.1DownloadDoc
novoSNP is a program that will help you find variations (SNPs and short INDELs) in resequencing projects. It takes a reference sequence and a number of sequencing trace files as input, and generates a list of possible variations with a quality score. novoSNP allows you to easily filter, sort and check the variations found visually and keep track of your verifications.

Remarque
Run Unix # novosnp2.0.1Run Web #

VersionMAJ

PSMC

0.6.52016-04-07DownloadDoc
This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.

Remarque
Run Unix # psmc [options] input.txtRun Web #

VersionMAJ

SAMtools

1.22015-04-15DownloadDoc
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Remarque
Run Unix # samtools [options]Run Web #

VersionMAJ

Vcflib

2017-03-10DownloadDoc
A C++ library for parsing and manipulating VCF files.

Remarque
Run Unix # Run Web #

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