{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:24Z","timestamp":1772138064530,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,4,4]],"date-time":"2024-04-04T00:00:00Z","timestamp":1712188800000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","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":[[2024,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Long-read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or nonunique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Pacybara, freely available at https:\/\/github.com\/rothlab\/pacybara, is implemented using R, Python, and bash for Linux. It runs on GNU\/Linux HPC clusters via Slurm, PBS, or GridEngine schedulers. A single-machine simplex version is also available.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae182","type":"journal-article","created":{"date-parts":[[2024,4,2]],"date-time":"2024-04-02T18:51:32Z","timestamp":1712083892000},"source":"Crossref","is-referenced-by-count":8,"title":["Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1628-9390","authenticated-orcid":false,"given":"Jochen","family":"Weile","sequence":"first","affiliation":[{"name":"Lunenfeld-Tanenbaum Research Institute, Sinai Health , Toronto, ON M5G 1X5, Canada"},{"name":"Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Molecular Genetics, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"}]},{"given":"Gabrielle","family":"Ferra","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States"}]},{"given":"Gabriel","family":"Boyle","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States"}]},{"given":"Sriram","family":"Pendyala","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States"}]},{"given":"Clara","family":"Amorosi","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4032-8871","authenticated-orcid":false,"given":"Chiann-Ling","family":"Yeh","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States"}]},{"given":"Atina G","family":"Cote","sequence":"additional","affiliation":[{"name":"Lunenfeld-Tanenbaum Research Institute, Sinai Health , Toronto, ON M5G 1X5, Canada"},{"name":"Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Molecular Genetics, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"}]},{"given":"Nishka","family":"Kishore","sequence":"additional","affiliation":[{"name":"Lunenfeld-Tanenbaum Research Institute, Sinai Health , Toronto, ON M5G 1X5, Canada"},{"name":"Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Molecular Genetics, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"}]},{"given":"Daniel","family":"Tabet","sequence":"additional","affiliation":[{"name":"Lunenfeld-Tanenbaum Research Institute, Sinai Health , Toronto, ON M5G 1X5, Canada"},{"name":"Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Molecular Genetics, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"}]},{"given":"Warren","family":"van Loggerenberg","sequence":"additional","affiliation":[{"name":"Lunenfeld-Tanenbaum Research Institute, Sinai Health , Toronto, ON M5G 1X5, Canada"},{"name":"Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Molecular Genetics, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"},{"name":"Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15213, United States"}]},{"given":"Ashyad","family":"Rayhan","sequence":"additional","affiliation":[{"name":"Lunenfeld-Tanenbaum Research Institute, Sinai Health , Toronto, ON M5G 1X5, Canada"},{"name":"Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Molecular Genetics, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"}]},{"given":"Douglas M","family":"Fowler","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States"},{"name":"Department of Bioengineering, University of Washington , Seattle, WA 98195, United States"},{"name":"Brotman Baty Institute for Precision Medicine , Seattle, WA 98195, United States"}]},{"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, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6628-649X","authenticated-orcid":false,"given":"Frederick P","family":"Roth","sequence":"additional","affiliation":[{"name":"Lunenfeld-Tanenbaum Research Institute, Sinai Health , Toronto, ON M5G 1X5, Canada"},{"name":"Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Molecular Genetics, University of Toronto , Toronto, ON M5S 3E1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"},{"name":"Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15213, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,4,3]]},"reference":[{"key":"2024041704594846800_btae182-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 J Hum Genet"},{"key":"2024041704594846800_btae182-B2","author":"Boyle","year":"2023"},{"key":"2024041704594846800_btae182-B3","doi-asserted-by":"crossref","first-page":"6968","DOI":"10.1038\/s41467-022-34630-w","article-title":"Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny","volume":"13","author":"Edgar","year":"2022","journal-title":"Nat Commun"},{"key":"2024041704594846800_btae182-B4","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nmeth.1416","article-title":"Parallel, tag-directed assembly of locally derived short sequence 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