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

Abstract read

In one paragraph

Article in Bioinformatics advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it

0cells of the map it votes in

2citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

Multiple Eurasian Origins and Admixture Shaped the Genomic Legacy of the House Mouse Invasion in Africa.Molecular ecology · 2026
Article
PopGLen-a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods.Bioinformatics (Oxford, England) · 2025
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Zehua T ZhouDepartment of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.

Gregory L OwensDepartment of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada.

Wesley A LarsonNational Marine Fisheries Service, Alaska Fisheries Science Center, National Oceanographic and Atmospheric Administration, Auke Bay Laboratories, Juneau, AK 99801, USA.

Runyang Nicolas LouDepartment of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.ORCID https://orcid.org/0000-0002-1568-0024

Peter H SudmantDepartment of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.ORCID https://orcid.org/0000-0002-9573-8248

Funding

The evolution and diversity of mutation, molecular fidelity, and genome structureR35GM142916 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Peter Heshedahl Sudmant · 2021 to 2026

$2.5M

NIGMS NIH HHS R35 GM142916

6 · The paper itself

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).

Identifiers

PMID39006965

DOI10.1093/bioadv/vbae098

PMCPMC11246161

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.