{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T14:30:12Z","timestamp":1775140212560,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,8,26]],"date-time":"2024-08-26T00:00:00Z","timestamp":1724630400000},"content-version":"vor","delay-in-days":25,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100016662","name":"Carnegie Institution for Science","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016662","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institutes of Health\u2019s Early Investigator","award":["#1DP5OD029506-01"],"award-info":[{"award-number":["#1DP5OD029506-01"]}]},{"name":"University of California Berkeley, and the Howard Hughes Medical Institute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversity in wild populations, and genotype-to-phenotype mapping. Here, we present grenedalf, a command line tool written in C++ that implements common population genetic statistics such as \u03b8, Tajima\u2019s D, and FST for Pool sequencing. It is orders of magnitude faster than current tools, and is focused on providing usability and scalability, while also offering a plethora of input file formats and convenience options.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>grenedalf is published under the GPL-3, and freely available at github.com\/lczech\/grenedalf.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae508","type":"journal-article","created":{"date-parts":[[2024,8,25]],"date-time":"2024-08-25T01:26:21Z","timestamp":1724549181000},"source":"Crossref","is-referenced-by-count":36,"title":["grenedalf: population genetic statistics for the next generation of pool sequencing"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1340-9644","authenticated-orcid":false,"given":"Lucas","family":"Czech","sequence":"first","affiliation":[{"name":"Department of Plant Biology, Carnegie Institution for Science , Stanford, CA 94305, United States"},{"name":"Section for GeoGenetics, Globe Institute, University of Copenhagen , 1350 K\u00f8benhavn, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3199-1447","authenticated-orcid":false,"given":"Jeffrey P","family":"Spence","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University , Stanford, CA 94305, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5711-0700","authenticated-orcid":false,"given":"Mois\u00e9s","family":"Exp\u00f3sito-Alonso","sequence":"additional","affiliation":[{"name":"Department of Plant Biology, Carnegie Institution for Science , Stanford, CA 94305, United States"},{"name":"Department of Biology, Stanford University , Stanford, CA 94305, United States"},{"name":"Department of Global Ecology, Carnegie Institution for Science , Stanford, CA 94305, United States"},{"name":"Department of Integrative Biology, University of California Berkeley , Berkeley, CA 94720, United States"},{"name":"Howard Hughes Medical Institute, University of California Berkeley , Berkeley, CA 94720, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,8,26]]},"reference":[{"key":"2024082901041376000_btae508-B1","doi-asserted-by":"crossref","first-page":"3263","DOI":"10.1093\/bioinformatics\/btaa070","article-title":"Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data","volume":"36","author":"Czech","year":"2020","journal-title":"Bioinformatics"},{"key":"2024082901041376000_btae508-B2","doi-asserted-by":"crossref","first-page":"4809","DOI":"10.1093\/bioinformatics\/btac600","article-title":"grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads","volume":"38","author":"Czech","year":"2022","journal-title":"Bioinformatics"},{"key":"2024082901041376000_btae508-B3","doi-asserted-by":"crossref","DOI":"10.1101\/2022.02.02.477408","volume-title":"Monitoring rapid evolution of plant populations at scale with Pool-sequencing","author":"Czech","year":"2022"},{"key":"2024082901041376000_btae508-B4","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2024082901041376000_btae508-B5","doi-asserted-by":"crossref","first-page":"5561","DOI":"10.1111\/mec.12522","article-title":"Population genomics from Pool sequencing","volume":"22","author":"Ferretti","year":"2013","journal-title":"Mol Ecol"},{"key":"2024082901041376000_btae508-B6","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1101\/gr.114819.110","article-title":"Efficient storage of high throughput DNA sequencing data using reference-based compression","volume":"21","author":"Fritz","year":"2011","journal-title":"Genome Res"},{"key":"2024082901041376000_btae508-B7","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1111\/1755-0998.13557","article-title":"f-statistics estimation and admixture graph construction with Pool-Seq or allele count data using the R package poolfstat","volume":"22","author":"Gautier","year":"2022","journal-title":"Mol Ecol Resour"},{"key":"2024082901041376000_btae508-B8","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1534\/genetics.118.300900","article-title":"Measuring genetic differentiation from pool-seq data","volume":"210","author":"Hivert","year":"2018","journal-title":"Genetics"},{"key":"2024082901041376000_btae508-B9","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1093\/genetics\/132.2.583","article-title":"Estimation of levels of gene flow from DNA sequence data","volume":"132","author":"Hudson","year":"1992","journal-title":"Genetics"},{"key":"2024082901041376000_btae508-B10","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1093\/molbev\/mst016","article-title":"Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data","volume":"30","author":"Kessner","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2024082901041376000_btae508-B11","doi-asserted-by":"crossref","first-page":"e15925","DOI":"10.1371\/journal.pone.0015925","article-title":"PoPoolation: A toolbox for population genetic analysis of next generation sequencing data from pooled individuals","volume":"6","author":"Kofler","year":"2011","journal-title":"PLoS One"},{"key":"2024082901041376000_btae508-B12","doi-asserted-by":"crossref","first-page":"3435","DOI":"10.1093\/bioinformatics\/btr589","article-title":"PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)","volume":"27","author":"Kofler","year":"2011","journal-title":"Bioinformatics"},{"key":"2024082901041376000_btae508-B13","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2024082901041376000_btae508-B14","doi-asserted-by":"crossref","first-page":"3321","DOI":"10.1073\/pnas.70.12.3321","article-title":"Analysis of gene diversity in subdivided populations","volume":"70","author":"Nei","year":"1973","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024082901041376000_btae508-B15","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1038\/nrg3803","article-title":"Sequencing pools of individuals\u2013mining genome-wide polymorphism data without big funding","volume":"15","author":"Schl\u00f6tterer","year":"2014","journal-title":"Nat Rev Genet"},{"key":"2024082901041376000_btae508-B16","doi-asserted-by":"crossref","first-page":"4159","DOI":"10.1534\/g3.119.400755","article-title":"Accurate allele frequencies from ultra-low coverage Pool-Seq samples in evolve-and-resequence experiments","volume":"9","author":"Tilk","year":"2019","journal-title":"G3 (Bethesda)"},{"key":"2024082901041376000_btae508-B17","doi-asserted-by":"crossref","first-page":"10015","DOI":"10.1038\/s41598-021-89495-8","article-title":"The SoftWipe tool and benchmark for assessing coding standards adherence of scientific software","volume":"11","author":"Zapletal","year":"2021","journal-title":"Sci Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae508\/58922813\/btae508.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae508\/58954867\/btae508.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae508\/58954867\/btae508.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,29]],"date-time":"2024-08-29T01:05:41Z","timestamp":1724893541000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae508\/7741639"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,8]]},"references-count":17,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2024,8,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae508","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,8]]},"published":{"date-parts":[[2024,8]]},"article-number":"btae508"}}