loco-pipe: an automated pipeline for population genomics with low-coverage whole-genome sequencing

Zehua T Zhou; Gregory L Owens; Wesley A Larson; Runyang Nicolas Lou; Peter H Sudmant

doi:10.1093/bioadv/vbae098

loco-pipe: an automated pipeline for population genomics with low-coverage whole-genome sequencing

Bioinform Adv. 2024 Jul 11;4(1):vbae098. doi: 10.1093/bioadv/vbae098. eCollection 2024.

Authors

Zehua T Zhou¹, Gregory L Owens², Wesley A Larson³, Runyang Nicolas Lou¹, Peter H Sudmant^{1

4}

Affiliations

¹ Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
² Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada.
³ National Marine Fisheries Service, Alaska Fisheries Science Center, National Oceanographic and Atmospheric Administration, Auke Bay Laboratories, Juneau, AK 99801, USA.
⁴ Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA.

Abstract

Summary: We developed loco-pipe, a Snakemake pipeline that seamlessly streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data. loco-pipe is highly automated, easily customizable, massively parallelized, and thus is a valuable tool for both new and experienced users of lcWGS.

Availability and implementation: loco-pipe is published under the GPLv3. It is freely available on GitHub (github.com/sudmantlab/loco-pipe) and archived on Zenodo (doi.org/10.5281/zenodo.10425920).