CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data.

ABSTRACT: Chloroplasts are photosynthetic organelles in algal and plant cells that contain their own genome. Chloroplast genomes are commonly used in evolutionary studies and taxonomic identification and are increasingly becoming a target for crop improvement studies. As DNA sequencing becomes more affordable, researchers are collecting vast swathes of high-quality whole-genome sequence data from laboratory and field settings alike. Whole tissue read libraries sequenced with the primary goal of understanding the nuclear genome will inadvertently contain many reads derived from the chloroplast genome. These whole-genome, whole-tissue read libraries can additionally be used to assemble chloroplast genomes with little to no extra cost. While several tools exist that make use of short-read second genera

SUBMITTER: Phillips AL 

PROVIDER: S-EPMC10883564 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature