A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics

Abstract

The increasing availability of short‐read whole genome sequencing (WGS) provides unprecedented opportunities to study ecological and evolutionary processes. Although loci of interest can be extracted from WGS data and combined with target sequence data, this requires suitable bioinformatic workflows. Here, we test different assembly and locus extraction strategies and implement them into secapr , a pipeline that processes short‐read data into multilocus alignments for phylogenetics and molecular ecology analyses. We integrate the processing of data from low‐coverage WGS ( k mer simultaneously for assembly results in the highest yield of extracted loci from de novo assembled contigs, while data sets derived from sequencing read depths as low as 5× recovers the expected species relationships in phylogenetic trees. By making the tested assembly approaches available in the secapr pipeline, we hope to inspire future studies to incorporate complementary data and make an informed choice on the optimal assembly strategy.

Bibliographic Information