{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T05:30:26Z","timestamp":1781155826483,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010137","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,4,27]],"date-time":"2023-04-27T00:00:00Z","timestamp":1682553600000}}],"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2023,4,17]],"date-time":"2023-04-17T00:00:00Z","timestamp":1681689600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R21-AI137433"],"award-info":[{"award-number":["R21-AI137433"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35-GM134922"],"award-info":[{"award-number":["R35-GM134922"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01- AI142572"],"award-info":[{"award-number":["R01- AI142572"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000861","name":"Burroughs Wellcome Fund","doi-asserted-by":"publisher","award":["1012376"],"award-info":[{"award-number":["1012376"]}],"id":[{"id":"10.13039\/100000861","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales\u2014precisely the scales at which these processes occur\u2014microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present <jats:monospace specific-use=\"no-wrap\">swga2.0<\/jats:monospace>, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, <jats:monospace specific-use=\"no-wrap\">swga2.0<\/jats:monospace> incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, <jats:monospace specific-use=\"no-wrap\">swga2.0<\/jats:monospace> optimizes primer set search and evaluation strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime. Here we describe the <jats:monospace specific-use=\"no-wrap\">swga2.0<\/jats:monospace> pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluate the novel <jats:monospace specific-use=\"no-wrap\">swga2.0<\/jats:monospace> pipeline by designing primer sets that successfully amplify <jats:italic>Prevotella melaninogenica<\/jats:italic>, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010137","type":"journal-article","created":{"date-parts":[[2023,4,17]],"date-time":"2023-04-17T17:39:08Z","timestamp":1681753148000},"page":"e1010137","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":20,"title":["A fast machine-learning-guided primer design pipeline for selective whole genome amplification"],"prefix":"10.1371","volume":"19","author":[{"given":"Jane A.","family":"Dwivedi-Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary 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