Title | Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples |
Publication Type | Journal Article |
Year of Publication | 2013 |
Authors | Boitard, S, Kofler, R, Francoise, P, Robelin, D, Schlötterer, C, Futschik, A |
Journal | Molecular Ecology Resources |
Pagination | n/a–n/a |
ISSN | 1755-0998 |
Keywords | allele 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/. |
URL | http://dx.doi.org/10.1111/1755-0998.12063 |
DOI | 10.1111/1755-0998.12063 |
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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