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

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

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

Afiliación

Zhou ZT; Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
Owens GL; Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada.
Larson WA; National Marine Fisheries Service, Alaska Fisheries Science Center, National Oceanographic and Atmospheric Administration, Auke Bay Laboratories, Juneau, AK 99801, USA.
Lou RN; Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
Sudmant PH; Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.

Bioinform Adv ; 4(1): vbae098, 2024.

Article en En | MEDLINE | ID: mdl-39006965

ABSTRACT

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).

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Bioinform Adv Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido

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