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Marc Bras

National,  COM (posters)

Jobim 2010 - Montpelier

07 Sep 2010   Development of a workflow for SNP detection with Galaxy (MAPHiTS).
Poster_Jobim_2010_Bras_Arnoux

Nacer Mohellibi, Nathalie Choisne, Olivier Inizan, Delphine Steinbach, Hadi Quesneville

A Single-Nucleotide Polymorphism (SNP) is a DNA sequence variation. It can be
used as a marker to characterize genetic variations between lineages. They can
be used to detect complex traits such as those involved in diseases or
agronomical performance.
The URGI platform developed a pipeline for SNPs detection from short reads,
integrated in the Galaxy[1] workflow manager. Galaxy allows, through a web
page, to chain different tools graphically. In addition, a large number of
workflows can be built and shared.
From a reference genome and a set of short reads (single-end or pair-ends), our
workflow use BWA[2], SAMtools[3], VarScan[4] and Tablet[5] to predict SNPs and
indels with number of filters, such as genome coverage, allele frequency, pValue.

 


[Download pdf: 1.30 MB]
Update: 10 May 2011
Creation date: 16 Sep 2010
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