{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T17:16:21Z","timestamp":1775841381886,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009802","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,2,3]],"date-time":"2022-02-03T00:00:00Z","timestamp":1643846400000}}],"reference-count":29,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2022,1,24]],"date-time":"2022-01-24T00:00:00Z","timestamp":1642982400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1175797"],"award-info":[{"award-number":["OPP1175797"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Australian Government Research Training Program Scholarship"},{"DOI":"10.13039\/100008717","name":"Sylvia and Charles Viertel Charitable Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008717","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these errors, but most rely on short-read alignment which is unreliable in repeat regions. Errors in such regions are therefore challenging to fix and often remain after short-read polishing. Here we introduce Polypolish, a new short-read polisher which uses all-per-read alignments to repair errors in repeat sequences that other polishers cannot. Polypolish performed well in benchmarking tests using both simulated and real reads, and it almost never introduced errors during polishing. The best results were achieved by using Polypolish in combination with other short-read polishers.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1009802","type":"journal-article","created":{"date-parts":[[2022,1,24]],"date-time":"2022-01-24T13:38:37Z","timestamp":1643031517000},"page":"e1009802","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":637,"title":["Polypolish: Short-read polishing of long-read bacterial genome assemblies"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8349-0778","authenticated-orcid":true,"given":"Ryan R.","family":"Wick","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3949-2471","authenticated-orcid":true,"given":"Kathryn E.","family":"Holt","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,1,24]]},"reference":[{"key":"pcbi.1009802.ref001","first-page":"110","volume":"23","author":"S Koren","journal-title":"One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly"},{"issue":"2138","key":"pcbi.1009802.ref002","volume":"8","author":"RR Wick","journal-title":"Benchmarking of long-read assemblers for prokaryote whole genome sequencing"},{"issue":"1","key":"pcbi.1009802.ref003","first-page":"266","volume":"22","author":"RR Wick","journal-title":"Trycycler: consensus long-read assemblies for bacterial genomes"},{"issue":"2","key":"pcbi.1009802.ref004","first-page":"124","volume":"37","author":"M Watson","journal-title":"Errors in long-read assemblies can critically affect protein prediction"},{"issue":"4","key":"pcbi.1009802.ref005","first-page":"338","volume":"36","author":"M Jain","journal-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads"},{"issue":"6","key":"pcbi.1009802.ref006","first-page":"e1005595","volume":"13","author":"RR Wick","journal-title":"Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads"},{"issue":"14","key":"pcbi.1009802.ref007","volume":"22","author":"P Zhang","journal-title":"Comparison of De Novo Assembly Strategies for Bacterial Genomes"},{"key":"pcbi.1009802.ref008","unstructured":"Wright C, Wykes M. 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