{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T17:47:06Z","timestamp":1772819226625,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,3,11]],"date-time":"2025-03-11T00:00:00Z","timestamp":1741651200000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Strategic Research Area \u201cBiodiversity and Ecosystem Services in a Changing Climate"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>PopGLen is a Snakemake workflow for performing population genomic analyses within a genotype-likelihood framework, integrating steps for raw sequence processing of both historical and modern DNA, quality control, multiple filtering schemes, and population genomic analysis. Currently, the population genomic analyses included allow for estimating linkage disequilibrium, kinship, genetic diversity, genetic differentiation, population structure, inbreeding, and allele frequencies. Through Snakemake, it is highly scalable, and all steps of the workflow are automated, with results compiled into an HTML report. PopGLen provides an efficient, customizable, and reproducible option for analyzing population genomic datasets across a wide variety of organisms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PopGLen is available under GPLv3 with code, documentation, and a tutorial at https:\/\/github.com\/zjnolen\/PopGLen. An example HTML report using the tutorial dataset is included in the Supplementary Material.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf105","type":"journal-article","created":{"date-parts":[[2025,3,11]],"date-time":"2025-03-11T13:45:26Z","timestamp":1741700726000},"source":"Crossref","is-referenced-by-count":2,"title":["PopGLen\u2014a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8146-8016","authenticated-orcid":false,"given":"Zachary J","family":"Nolen","sequence":"first","affiliation":[{"name":"Department of Biology, Lund University , Lund 22 362,","place":["Sweden"]}]}],"member":"286","published-online":{"date-parts":[[2025,3,11]]},"reference":[{"key":"2025032423322671300_btaf105-B2","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1101\/gr.154831.113","article-title":"Estimating and interpreting FST: the impact of rare variants","volume":"23","author":"Bhatia","year":"2013","journal-title":"Genome Res"},{"key":"2025032423322671300_btaf105-B3","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B4","doi-asserted-by":"crossref","first-page":"2580","DOI":"10.1093\/bioinformatics\/btx192","article-title":"BioContainers: an open-source and community-driven framework for software standardization","volume":"33","author":"da Veiga Leprevost","year":"2017","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"2025032423322671300_btaf105-B6","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.tree.2017.12.002","article-title":"Quantifying temporal genomic erosion in endangered species","volume":"33","author":"D\u00edez-Del-Molino","year":"2018","journal-title":"Trends Ecol Evol"},{"key":"2025032423322671300_btaf105-B7","doi-asserted-by":"crossref","first-page":"e30377","DOI":"10.1371\/journal.pone.0030377","article-title":"Fast computation and applications of genome mappability","volume":"7","author":"Derrien","year":"2012","journal-title":"PLoS One"},{"key":"2025032423322671300_btaf105-B8","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B9","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"Flynn","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025032423322671300_btaf105-B10","doi-asserted-by":"crossref","first-page":"3855","DOI":"10.1093\/bioinformatics\/btz200","article-title":"ngsLD: evaluating linkage disequilibrium using genotype likelihoods","volume":"35","author":"Fox","year":"2019","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B11","doi-asserted-by":"crossref","first-page":"2678","DOI":"10.1093\/bioinformatics\/bts503","article-title":"Qualimap: evaluating next-generation sequencing alignment data","volume":"28","author":"Garc\u00eda-Alcalde","year":"2012","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B12","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1111\/1755-0998.13171","article-title":"Evaluation of model fit of inferred admixture proportions","volume":"20","author":"Garcia-Erill","year":"2020","journal-title":"Mol Ecol Resources"},{"key":"2025032423322671300_btaf105-B13","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"Bioconda: sustainable and comprehensive software distribution for the life sciences","volume":"15","author":"Gr\u00fcning","year":"2018","journal-title":"Nat Methods"},{"key":"2025032423322671300_btaf105-B14","doi-asserted-by":"crossref","first-page":"giz034","DOI":"10.1093\/gigascience\/giz034","article-title":"Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding","volume":"8","author":"Hangh\u00f8j","year":"2019","journal-title":"Gigascience"},{"key":"2025032423322671300_btaf105-B15","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1093\/bioinformatics\/btt193","article-title":"mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters","volume":"29","author":"J\u00f3nsson","year":"2013","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B16","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1101\/gr.176552.114","article-title":"An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data","volume":"25","author":"Jun","year":"2015","journal-title":"Genome Res"},{"key":"2025032423322671300_btaf105-B17","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1186\/s12859-022-04757-0","article-title":"GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species","volume":"23","author":"Kutschera","year":"2022","journal-title":"BMC Bioinformatics"},{"key":"2025032423322671300_btaf105-B18","author":"Li"},{"key":"2025032423322671300_btaf105-B19","doi-asserted-by":"crossref","first-page":"5966","DOI":"10.1111\/mec.16077","article-title":"A beginner\u2019s guide to low-coverage whole genome sequencing for population genomics","volume":"30","author":"Lou","year":"2021","journal-title":"Mol Ecol"},{"key":"2025032423322671300_btaf105-B20","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.ajhg.2008.08.007","article-title":"Runs of homozygosity in European populations","volume":"83","author":"McQuillan","year":"2008","journal-title":"Am J Hum Genet"},{"key":"2025032423322671300_btaf105-B21","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1534\/genetics.118.301336","article-title":"Inferring population structure and admixture proportions in low-depth NGS data","volume":"210","author":"Meisner","year":"2018","journal-title":"Genetics"},{"key":"2025032423322671300_btaf105-B22","doi-asserted-by":"crossref","first-page":"33","DOI":"10.12688\/f1000research.29032.2","article-title":"Sustainable data analysis with snakemake [version 2; peer review: 2 approved]","volume":"10","author":"M\u00f6lder","year":"2021","journal-title":"F1000Res"},{"key":"2025032423322671300_btaf105-B23","doi-asserted-by":"crossref","first-page":"1919","DOI":"10.1093\/bioinformatics\/bts277","article-title":"BEDOPS: high-performance genomic feature operations","volume":"28","author":"Neph","year":"2012","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B24","doi-asserted-by":"crossref","first-page":"btad028","DOI":"10.1093\/bioinformatics\/btad028","article-title":"Mapache: a flexible pipeline to map ancient DNA","volume":"39","author":"Neuenschwander","year":"2023","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B25","doi-asserted-by":"crossref","first-page":"3652","DOI":"10.1093\/bioinformatics\/btab190","article-title":"DamageProfiler: fast damage pattern calculation for ancient DNA","volume":"37","author":"Neukamm","year":"2021","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B26","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/nrg2986","article-title":"Genotype and SNP calling from next-generation sequencing data","volume":"12","author":"Nielsen","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2025032423322671300_btaf105-B27","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1016\/j.cub.2015.04.007","article-title":"Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth","volume":"25","author":"Palkopoulou","year":"2015","journal-title":"Curr Biol"},{"key":"2025032423322671300_btaf105-B28","doi-asserted-by":"crossref","first-page":"1862","DOI":"10.1016\/j.cub.2021.01.064","article-title":"High genetic diversity and low differentiation reflect the ecological versatility of the African leopard","volume":"31","author":"Pe\u010dnerov\u00e1","year":"2021","journal-title":"Curr Biol"},{"key":"2025032423322671300_btaf105-B29","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/s13059-016-0918-z","article-title":"EAGER: efficient ancient genome reconstruction","volume":"17","author":"Peltzer","year":"2016","journal-title":"Genome Biol"},{"key":"2025032423322671300_btaf105-B30","doi-asserted-by":"crossref","first-page":"3687","DOI":"10.1093\/bioinformatics\/btaa222","article-title":"GenMap: ultra-fast computation of genome mappability","volume":"36","author":"Pockrandt","year":"2020","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B31","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B32","doi-asserted-by":"crossref","first-page":"1860","DOI":"10.1111\/mec.16851","article-title":"Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo","volume":"32","author":"Quinn","year":"2023","journal-title":"Mol Ecol"},{"key":"2025032423322671300_btaf105-B33","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2017"},{"key":"2025032423322671300_btaf105-B34","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1038\/nprot.2014.063","article-title":"Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX","volume":"9","author":"Schubert","year":"2014","journal-title":"Nat Protoc"},{"key":"2025032423322671300_btaf105-B35","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1534\/genetics.113.154138","article-title":"Estimating individual admixture proportions from next generation sequencing data","volume":"195","author":"Skotte","year":"2013","journal-title":"Genetics"},{"key":"2025032423322671300_btaf105-B36","author":"Smit","year":"2013\u20132015"},{"key":"2025032423322671300_btaf105-B1","volume-title":"Genomics in the Cloud: Using Docker, GATK, and WDL in Terra","author":"Van der Auwera","year":"2020"},{"key":"2025032423322671300_btaf105-B37","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1093\/bioinformatics\/btw212","article-title":"Estimating IBD tracts from low coverage NGS data","volume":"32","author":"Vieira","year":"2016","journal-title":"Bioinformatics"},{"key":"2025032423322671300_btaf105-B38","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1111\/mec.14954","article-title":"Allele frequency-free inference of close familial relationships from genotypes or low-depth sequencing data","volume":"28","author":"Waples","year":"2019","journal-title":"Mol Ecol"},{"key":"2025032423322671300_btaf105-B39","doi-asserted-by":"crossref","first-page":"vbae098","DOI":"10.1093\/bioadv\/vbae098","article-title":"loco-pipe: an automated pipeline for population genomics with low-coverage whole-genome sequencing","volume":"4","author":"Zhou","year":"2024","journal-title":"Bioinform Adv"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf105\/62375473\/btaf105.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/3\/btaf105\/62375473\/btaf105.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/3\/btaf105\/62375473\/btaf105.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,29]],"date-time":"2025-03-29T04:52:39Z","timestamp":1743223959000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf105\/8069456"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":39,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf105","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,3]]},"published":{"date-parts":[[2025,3]]},"article-number":"btaf105"}}