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Mol Ecol Resour. 2013 Mar;13(2):337-40. doi: 10.1111/1755-0998.12063. Epub 2013 Jan 11.

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.

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1
Laboratoire de Génétique Cellulaire, INRA, 24 Chemin de Borde Rouge, Auzeville CS 52627, Castanet Tolosan Cedex, 31326, France. simon.boitard@toulouse.inra.fr

Abstract

Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for genome-wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool-seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool-Seq data. We introduce Pool-hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample. Pool-hmm includes several options that allow a flexible analysis of Pool-Seq data, and can be run in parallel on several processors. Source code and documentation for Pool-hmm is freely available at https://qgsp.jouy.inra.fr/.

PMID:
23311589
PMCID:
PMC3592992
DOI:
10.1111/1755-0998.12063
[Indexed for MEDLINE]
Free PMC Article
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