{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T03:57:06Z","timestamp":1781755026641,"version":"3.54.5"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,8,20]],"date-time":"2020-08-20T00:00:00Z","timestamp":1597881600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Error correction is a fundamental pre-processing step in many Next-Generation Sequencing (NGS) pipelines, in particular for de novo genome assembly. However, existing error correction methods either suffer from high false-positive rates since they break reads into independent k-mers or do not scale efficiently to large amounts of sequencing reads and complex genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present CARE\u2014an alignment-based scalable error correction algorithm for Illumina data using the concept of minhashing. Minhashing allows for efficient similarity search within large sequencing read collections which enables fast computation of high-quality multiple alignments. Sequencing errors are corrected by detailed inspection of the corresponding alignments. Our performance evaluation shows that CARE generates significantly fewer false-positive corrections than state-of-the-art tools (Musket, SGA, BFC, Lighter, Bcool, Karect) while maintaining a competitive number of true positives. When used prior to assembly it can achieve superior de novo assembly results for a number of real datasets. CARE is also the first multiple sequence alignment-based error corrector that is able to process a human genome Illumina NGS dataset in only 4\u2009h on a single workstation using GPU acceleration.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>CARE is open-source software written in C++ (CPU version) and in CUDA\/C++ (GPU version). It is licensed under GPLv3 and can be downloaded at https:\/\/github.com\/fkallen\/CARE.<\/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\/btaa738","type":"journal-article","created":{"date-parts":[[2020,8,14]],"date-time":"2020-08-14T15:29:09Z","timestamp":1597418949000},"page":"889-895","source":"Crossref","is-referenced-by-count":17,"title":["CARE: context-aware sequencing read error correction"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4516-6357","authenticated-orcid":false,"given":"Felix","family":"Kallenborn","sequence":"first","affiliation":[{"name":"Department of Computer Science, Johannes Gutenberg University , Mainz 55122, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Hildebrandt","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johannes Gutenberg University , Mainz 55122, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johannes Gutenberg University , Mainz 55122, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,8,20]]},"reference":[{"key":"2023051612181922700_btaa738-B1","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-52196-4","article-title":"Athena: automated tuning of k-mer based genomic error correction algorithms using language models","volume":"9","author":"Abdallah","year":"2019","journal-title":"Sci. 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