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