Data from: The impact of library preparation protocols on the accuracy of allele frequency estimates in Pool-Seq data

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.

混合个体测序（Pool-Seq）是一种经济高效的全基因组等位基因频率估算方法。鉴于整合多数据集开展元分析的重要性，本研究考察了不同基因组文库制备方案对等位基因频率估算一致性的影响。结果显示，等位基因频率估算的变异中，通常仅有不超过1%可归因于文库制备流程的差异。此外，测序读长对该估算一致性的影响同样微弱。迄今为止，对估算一致性影响最为显著的因素为测序覆盖度：将覆盖度从30倍提升至50倍，可使等位基因频率估算的一致性至少提升27%。综上，混合个体测序（Pool-Seq）的数据可轻松实现不同文库制备方法间的整合，但充足的测序覆盖度是获得可靠结果的关键。