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 (<30×) and target sequence capture into a flexible framework, while optimizing de novo contig assembly and loci extraction. Specifically, we test different assembly strategies by contrasting their ability to recover loci fro

SUBMITTER: G Ribeiro P 

PROVIDER: S-EPMC9298010 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature