title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data.
abstract: Sequencing pools of individuals (Pool-Seq) is a cost-effective method to determine genome-wide allele frequency estimates. Given the importance of meta-analyses combining data sets, we determined the influence of different genomic library preparation protocols on the consistency of allele frequency estimates. We found that typically no more than 1% of the variation in allele frequency estimates could be attributed to differences in library preparation. Also read length had only a minor effect on the consistency of allele frequency estimates. By far, the most pronounced influence could be attributed to sequence coverage. Increasing the coverage from 30- to 50-fold improved the consistency of allele frequency estimates by at least 27%. We conclude that Pool-Seq data can be easily combined across different library preparation methods, but sufficient sequence coverage is key to reliable results.
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria.
authors.forename: Robert
authors.initials: R
authors.lastname: Kofler
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria.
authors.forename: Viola
authors.initials: V
authors.lastname: Nolte
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Schlötterer
mesh_terms: D000818:Animals; D004330:Drosophila / Q000235:genetics*; D005787:Gene Frequency; D015723:Gene Library; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing
keywords: Drosophila; NGS libraries; Pool-Seq; population genetics-empirical