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

TitlePool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples
Publication TypeJournal Article
Year of Publication2013
AuthorsBoitard, S, Kofler, R, Francoise, P, Robelin, D, Schlötterer, C, Futschik, A
JournalMolecular Ecology Resources
Paginationn/a–n/a
ISSN1755-0998
Keywordsallele frequency spectrum, hidden Markov models, next generation sequencing, pooled DNA, selective sweeps.
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/.

URLhttp://dx.doi.org/10.1111/1755-0998.12063
DOI10.1111/1755-0998.12063