{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T22:15:39Z","timestamp":1774736139964,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Next-generation sequencing technologies produce short reads that are either de novo assembled or mapped to a reference genome. Genotypes and\/or single-nucleotide polymorphisms are then determined from the read composition at each site, which become the basis for many downstream analyses. However, for low sequencing depths, e.g. , there is considerable statistical uncertainty in the assignment of genotypes because of random sampling of homologous base pairs in heterozygotes and sequencing or alignment errors. Recently, several probabilistic methods have been proposed to account for this uncertainty and make accurate inferences from low quality and\/or coverage sequencing data.<\/jats:p><jats:p>We present ngsTools, a collection of programs to perform population genetics analyses from next-generation sequencing data. The methods implemented in these programs do not rely on single-nucleotide polymorphism or genotype calling and are particularly suitable for low sequencing depth data.<\/jats:p><jats:p>Availability: Programs included in ngsTools are implemented in C\/C++ and are freely available for noncommercial use at https:\/\/github.com\/mfumagalli\/ngsTools.<\/jats:p><jats:p>Contact: \u00a0mfumagalli82@gmail.com<\/jats:p><jats:p>Supplementary Information: \u00a0Supplementary materials are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu041","type":"journal-article","created":{"date-parts":[[2014,1,24]],"date-time":"2014-01-24T01:25:22Z","timestamp":1390526722000},"page":"1486-1487","source":"Crossref","is-referenced-by-count":248,"title":["<i>ngsTools<\/i>: methods for population genetics analyses from next-generation sequencing data"],"prefix":"10.1093","volume":"30","author":[{"given":"Matteo","family":"Fumagalli","sequence":"first","affiliation":[{"name":"1 Department of Integrative Biology, 2Department of Statistics, University of California, Berkeley, CA 94720, USA and 3Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark"}]},{"given":"Filipe G.","family":"Vieira","sequence":"additional","affiliation":[{"name":"1 Department of Integrative Biology, 2Department of Statistics, University of California, Berkeley, CA 94720, USA and 3Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark"}]},{"given":"Tyler","family":"Linderoth","sequence":"additional","affiliation":[{"name":"1 Department of Integrative Biology, 2Department of Statistics, University of California, Berkeley, CA 94720, USA and 3Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark"}]},{"given":"Rasmus","family":"Nielsen","sequence":"additional","affiliation":[{"name":"1 Department of Integrative Biology, 2Department of Statistics, University of California, Berkeley, CA 94720, USA and 3Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark"},{"name":"1 Department of Integrative Biology, 2Department of Statistics, University of California, Berkeley, CA 94720, USA and 3Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark"},{"name":"1 Department of Integrative Biology, 2Department of Statistics, University of California, Berkeley, CA 94720, USA and 3Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2014,1,23]]},"reference":[{"key":"2023041302471424900_","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1534\/genetics.113.154740","article-title":"Quantifying population genetic differentiation from next-generation sequencing data","volume":"195","author":"Fumagalli","year":"2013","journal-title":"Genetics"},{"key":"2023041302471424900_","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nature11532","article-title":"A map of rice genome variation reveals the origin of cultivated rice","volume":"490","author":"Huang","year":"2012","journal-title":"Nature"},{"key":"2023041302471424900_","doi-asserted-by":"crossref","first-page":"e37558","DOI":"10.1371\/journal.pone.0037558","article-title":"SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data","volume":"7","author":"Nielsen","year":"2012","journal-title":"PLoS One"},{"key":"2023041302471424900_","doi-asserted-by":"crossref","first-page":"1852","DOI":"10.1101\/gr.157388.113","article-title":"Estimating inbreeding coefficients from ngs data: impact on genotype calling and allele frequency estimation","volume":"23","author":"Vieira","year":"2013","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/10\/1486\/49860456\/bioinformatics_30_10_1486.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/10\/1486\/49860456\/bioinformatics_30_10_1486.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T00:35:36Z","timestamp":1688949336000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/10\/1486\/267009"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1,23]]},"references-count":4,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2014,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu041","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,5,15]]},"published":{"date-parts":[[2014,1,23]]}}}