Patchwork: alignment-based retrieval and concatenation of phylogenetic markers from genomic data

MotivationIncreased output from the latest short-read sequencers makes low-coverage whole-genome sequencing (LC-WGS) an increasingly affordable approach to large-scale phylogenetics. Despite offering several advantages over prevailing sequencing strategies, few tools exist to work with this data type within a phylogenomic context. Due to the fragmented nature of LC-WGS genomes, their use have mostly been restricted to easy-to-assemble, high-copy-number regions such as organelle genomes and or ribosomal genes. ResultsWe here present a new method for mining phylogenetic markers directly from an assembled genome. Homologous regions are obtained via an alignment search, followed by a "hit-stitching" phase, in which adjacent or overlapping regions are concatenated together. Finally, a novel sliding window technique is used to trim non-coding regions from the alignments. We demonstrate the utility of Patchwork by recovering near-universal single-copy orthologs (USCOs) in the annelid Dimorphilus gyrociliatus. AvailabilityPatchwork is available from Github under the GNU General Public license version 3. Contactfelix.thalen@uni-goettingen.de Supplementary informationSupplementary data are available at github.com/Animal-Evolution-and-Biodiversity/benchmarking-patchwork.