Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data.

ABSTRACT: Low-coverage whole-genome sequencing (also known as "genome skimming") is becoming an increasingly affordable approach to large-scale phylogenetic analyses. While already routinely used to recover organellar genomes, genome skimming is rather rarely utilized for recovering single-copy nuclear markers. One reason might be that only few tools exist to work with this data type within a phylogenomic context, especially to deal with fragmented genome assemblies. We here present a new software tool called Patchwork for mining phylogenetic markers from highly fragmented short-read assemblies as well as directly from sequence reads. Patchwork is an alignment-based tool that utilizes the sequence aligner DIAMOND and is written in the programming language Julia. Homologous regions are obtained via a

SUBMITTER: Thalen F 

PROVIDER: S-EPMC10735302 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature