{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:12Z","timestamp":1772138052002,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2022,3,21]],"date-time":"2022-03-21T00:00:00Z","timestamp":1647820800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Institute of General Medical Sciences of the National Institutes of Health","award":["R01 GM132162"],"award-info":[{"award-number":["R01 GM132162"]}]},{"name":"National Institute of General Medical Sciences of the National Institutes of Health","award":["R01 GM101091"],"award-info":[{"award-number":["R01 GM101091"]}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute of the NIH","doi-asserted-by":"crossref","award":["T32 HG00035"],"award-info":[{"award-number":["T32 HG00035"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Science Foundation Graduate Research Fellowships Program","award":["DGE-1762114"],"award-info":[{"award-number":["DGE-1762114"]}]},{"name":"Bonita and David Brewer Fellowship"},{"name":"Faculty Scholar grant from the Howard Hughes Medical Institute"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Use of PacBio sequencing for characterizing barcoded libraries of genetic variants is on the rise. However, current approaches in resolving PacBio sequencing artifacts can result in a high number of incorrectly identified or unusable reads. Here, we developed a PacBio Read Alignment Tool (PacRAT) that improves the accuracy of barcode-variant mapping through several steps of read alignment and consensus calling. To quantify the performance of our approach, we simulated PacBio reads from eight variant libraries of various lengths and showed that PacRAT improves the accuracy in pairing barcodes and variants across these libraries. Analysis of real (non-simulated) libraries also showed an increase in the number of reads that can be used for downstream analyses when using PacRAT.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PacRAT is written in Python and is freely available (https:\/\/github.com\/dunhamlab\/PacRAT).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplemental data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac165","type":"journal-article","created":{"date-parts":[[2022,3,19]],"date-time":"2022-03-19T00:10:18Z","timestamp":1647648618000},"page":"2927-2929","source":"Crossref","is-referenced-by-count":11,"title":["PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4032-8871","authenticated-orcid":false,"given":"Chiann-Ling C","family":"Yeh","sequence":"first","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, USA"}]},{"given":"Clara J","family":"Amorosi","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, USA"}]},{"given":"Soyeon","family":"Showman","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, USA"},{"name":"Molecular and Cellular Biology Program, University of Washington , Seattle, WA 98195, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9944-2666","authenticated-orcid":false,"given":"Maitreya J","family":"Dunham","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,3,21]]},"reference":[{"key":"2023020109071736600_btac165-B1","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1016\/j.ajhg.2021.07.001","article-title":"Massively parallel characterization of CYP2C9 variant enzyme activity and abundance","volume":"108","author":"Amorosi","year":"2021","journal-title":"Am. 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