{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T20:32:09Z","timestamp":1778877129596,"version":"3.51.4"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,11,28]],"date-time":"2019-11-28T00:00:00Z","timestamp":1574899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Although long-read sequencing technologies can produce genomes with long contiguity, they suffer from high error rates. Thus, we developed NextPolish, a tool that efficiently corrects sequence errors in genomes assembled with long reads. This new tool consists of two interlinked modules that are designed to score and count K-mers from high quality short reads, and to polish genome assemblies containing large numbers of base errors.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>When evaluated for the speed and efficiency using human and a plant (Arabidopsis thaliana) genomes, NextPolish outperformed Pilon by correcting sequence errors faster, and with a higher correction accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>NextPolish is implemented in C and Python. The source code is available from https:\/\/github.com\/Nextomics\/NextPolish.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz891","type":"journal-article","created":{"date-parts":[[2019,11,26]],"date-time":"2019-11-26T12:11:54Z","timestamp":1574770314000},"page":"2253-2255","source":"Crossref","is-referenced-by-count":1121,"title":["NextPolish: a fast and efficient genome polishing tool for long-read assembly"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8521-9161","authenticated-orcid":false,"given":"Jiang","family":"Hu","sequence":"first","affiliation":[{"name":"GrandOmics Biosciences , Beijing, 102200, China"}]},{"given":"Junpeng","family":"Fan","sequence":"additional","affiliation":[{"name":"GrandOmics Biosciences , Beijing, 102200, China"}]},{"given":"Zongyi","family":"Sun","sequence":"additional","affiliation":[{"name":"GrandOmics Biosciences , Beijing, 102200, China"}]},{"given":"Shanlin","family":"Liu","sequence":"additional","affiliation":[{"name":"GrandOmics Biosciences , Beijing, 102200, China"}]}],"member":"286","published-online":{"date-parts":[[2019,11,28]]},"reference":[{"key":"2023062300073219800_btz891-B1","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1038\/s41477-018-0289-4","article-title":"Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps","volume":"4","author":"Belser","year":"2018","journal-title":"Nat. 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