HybPhaser: a workflow for the detection and phasing of hybrids in target capture datasets

O_LIPremise of the study: Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into parental lineages when identified and phased. We developed HybPhaser to detect hybrids in target capture datasets and to phase reads according to haplotypes based on similarity and a phylogenetic framework. C_LIO_LIMethods and Results: HybPhaser is an extension to the HybPiper sequence assembly workflow. We used Angiosperms353 target capture data for Nepenthes including known hybrids to test the novel workflow. Reference mapping was used to record heterozygous sites and identify hybrid accessions that were phased by mapping sequence reads to multiple references. The parental lineages of known hybrids were confirmed and conflicting phylogenetic signal reduced, improving the outcomes of phylogenetic analysis. C_LIO_LIConclusions: HybPhaser is a novel pipeline for summarizing and optimizing target capture datasets, detecting hybrid accessions as well as paralogous genes, and generating phased accessions that can provide insights into reticulated evolution. C_LI