{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T19:14:58Z","timestamp":1675278898837},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,15]]},"abstract":"<jats:p>Summary: Whole-genome sequencing has revolutionized the study of genetics. Genotyping-by-sequencing is now a viable method of genotyping, yet the bioinformatics involved can be daunting if not prohibitive for some laboratories. Here we present ArrayMaker, a user-friendly tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole-genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms. Using this tool, geneticists with only basic computing ability can genotype samples at any desired list of markers, facilitating genome-wide association analysis, fine mapping, candidate variant assessment, data sharing and compatibility of data sourced from multiple technologies.<\/jats:p>\n               <jats:p>Availability and implementation: ArrayMaker is licensed under The MIT License and can be freely obtained at https:\/\/github.com\/cw2014\/ArrayMaker\/. The program is implemented in Perl and runs on Linux operating systems.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Contact: \u00a0cali.willet@sydney.edu.au<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu691","type":"journal-article","created":{"date-parts":[[2014,10,22]],"date-time":"2014-10-22T05:07:31Z","timestamp":1413954451000},"page":"599-601","source":"Crossref","is-referenced-by-count":1,"title":["Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker"],"prefix":"10.1093","volume":"31","author":[{"given":"Cali E.","family":"Willet","sequence":"first","affiliation":[{"name":"1 \u00a01Faculty of Veterinary Science and 2School of Information Technologies, University of Sydney, Sydney, New South Wales 2006, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bianca","family":"Haase","sequence":"additional","affiliation":[{"name":"1 \u00a01Faculty of Veterinary Science and 2School of Information Technologies, University of Sydney, Sydney, New South Wales 2006, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael A.","family":"Charleston","sequence":"additional","affiliation":[{"name":"1 \u00a01Faculty of Veterinary Science and 2School of Information Technologies, University of Sydney, Sydney, New South Wales 2006, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claire M.","family":"Wade","sequence":"additional","affiliation":[{"name":"1 \u00a01Faculty of Veterinary Science and 2School of Information Technologies, University of Sydney, Sydney, New South Wales 2006, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,10,21]]},"reference":[{"key":"2023020108564108100_btu691-B1","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1093\/bioinformatics\/btu067","article-title":"Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals","volume":"30","author":"Cheng","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020108564108100_btu691-B2","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":"2023020108564108100_btu691-B3","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a toolset for whole-genome association and population-based linkage analysis","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/4\/599\/49011016\/bioinformatics_31_4_599.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/4\/599\/49011016\/bioinformatics_31_4_599.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T18:42:51Z","timestamp":1675276971000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/4\/599\/2748232"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,10,21]]},"references-count":3,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2015,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu691","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,10,21]]}}}