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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.

SUBMITTER: Kofler R

PROVIDER: S-EPMC4744716 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data.

Kofler Robert R Nolte Viola V Schlötterer Christian C

Molecular ecology resources 20150609 1

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 ...[more]

PMID: 26014582

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