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.

SNP


VersionMAJ

freebayes

v1.1.0-1-gf15e66e2017-02-16DownloadDoc
FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

Remarque Citing freebayes: Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012
Run Unix # freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT] Run Web #

VersionMAJ

inGAP

2.7.82011-11-02DownloadDoc
This is a novel mining pipeline (2009), Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche/454 and Illumina reads with no restriction of read length.

Remarque
Run Unix # inGAPRun Web #

VersionMAJ

kSNP

2.1.22014-04-24DownloadDoc
Indentify SNPs in a set of genome sequences without the requirement of a reference sequence or a multiple sequence alignment. Reconstruction of SNP based phylogenies by maximum likelihood.

Remarque
Run Unix # kSNP -k kmer_length -f fasta -d output_directory [-p genomes4positions_list] [-u unassembled_genomes_list] [-m minimum_fraction_genomes_with_locus] [-G genbank.gbk] [-n num_CPU] [-j ] [-v ] [-c min_kmer_coverage] Run Web #

VersionMAJ

polyphred

5.02DownloadDoc
PolyPhred is a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions.

Remarque
Run Unix # polyphredRun Web #

VersionMAJ

TFM-Pvalue

-2014-01-14DownloadDoc
TFM-Pvalue is a software suite providing tools for computing the score threshold associated to a given P-value and the P-value associated to a given score threshold. It uses Position Weight Matrices, such as those available in the Transfac or Jaspar databases.

Remarque Efficient and accurate P-value computation for Position Weight Matrices H. Touzet and J.S. Varré Algorithms for Molecular Biology 2007, 2:15
Run Unix # Run Web #

VersionMAJ

VarScan

4.2.32017-02-16DownloadDoc
variant detection in massively parallel sequencing data 

Remarque
Run Unix # varscan [COMMAND] [OPTIONS] Run Web #

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