In this protocol paper, we review a set of methods developed in recent years for analyzing nuclear reads obtained from genome skimming. As the cost of sequencing drops, genome skimming (low-coverage shotgun sequencing of a sample) becomes increasingly a cost-effective method of measuring biodiversity at high resolution. While most practitioners only use assembled over-represented organelle reads from a genome skim, the vast majority of the reads are nuclear. Using assembly-free and alignment-free methods described in this protocol, we can compare samples to each other and reference genomes to compute distances, characterize underlying genomes, and infer evolutionary relationships.
Keywords: Bioinformatics; Genome sequencing; Genome skimming; Nuclear DNA; Short read archive (SRA).
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.