loco-pipe: an automated pipeline for population genomics with low-coverage whole-genome sequencing-Reference-Cited by-同舟云学术

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

Published:2024 Issue:1 Volume:4 Page:
ISSN:2635-0041
Container-title:Bioinformatics Advances
language:en
Short-container-title:

Author:

Zhou Zehua T¹,Owens Gregory L²,Larson Wesley A³,Lou Runyang Nicolas¹^ORCID,Sudmant Peter H¹⁴^ORCID

Affiliation:

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

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).

Funder

National Institute of General Medical Sciences

Vallee Scholars Award to PHS

Publisher

Oxford University Press (OUP)

Link

https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbae098/58514775/vbae098.pdf

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