{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T19:24:15Z","timestamp":1776367455529,"version":"3.51.2"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,4,21]],"date-time":"2020-04-21T00:00:00Z","timestamp":1587427200000},"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\/100012950","name":"Inria","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012950","id-type":"DOI","asserted-by":"publisher"}]},{"name":"INCEPTION project","award":["PIA\/ANR-16-CONV-0005"],"award-info":[{"award-number":["PIA\/ANR-16-CONV-0005"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Genome assembly is increasingly performed on long, uncorrected reads. Assembly quality may be degraded due to unfiltered chimeric reads; also, the storage of all read overlaps can take up to terabytes of disk space.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce two tools: yacrd for chimera removal and read scrubbing, and fpa for filtering out spurious overlaps. We show that yacrd results in higher-quality assemblies and is one hundred times faster than the best available alternative.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/natir\/yacrd and https:\/\/github.com\/natir\/fpa.<\/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\/btaa262","type":"journal-article","created":{"date-parts":[[2020,4,15]],"date-time":"2020-04-15T07:10:09Z","timestamp":1586934609000},"page":"3894-3896","source":"Crossref","is-referenced-by-count":75,"title":["yacrd and fpa: upstream tools for long-read genome assembly"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6694-6873","authenticated-orcid":false,"given":"Pierre","family":"Marijon","sequence":"first","affiliation":[{"name":"Department of Computer Science , Inria, Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL, Lille F-59000, France"}]},{"given":"Rayan","family":"Chikhi","sequence":"additional","affiliation":[{"name":"Department of Computational Biology , Institut Pasteur, C3BI USR 3756 IP CNRS, Paris, France"}]},{"given":"Jean-St\u00e9phane","family":"Varr\u00e9","sequence":"additional","affiliation":[{"name":"Univ. Lille , CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France"}]}],"member":"286","published-online":{"date-parts":[[2020,4,21]]},"reference":[{"key":"2023063011300190900_btaa262-B1","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nbt.4060","article-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads","volume":"36","author":"Jain","year":"2018","journal-title":"Nat. Biotechnol"},{"key":"2023063011300190900_btaa262-B2","author":"LaPierre","year":"2018"},{"key":"2023063011300190900_btaa262-B3","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","article-title":"Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences","volume":"32","author":"Li","year":"2016","journal-title":"Bioinformatics"},{"key":"2023063011300190900_btaa262-B4","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2023063011300190900_btaa262-B5","author":"Maio","year":"2019"},{"key":"2023063011300190900_btaa262-B6","volume-title":"Nat Methods","author":"Ruan","year":"2019"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa262\/33238586\/btaa262.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/12\/3894\/50746424\/bioinformatics_36_12_3894.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/12\/3894\/50746424\/bioinformatics_36_12_3894.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T07:30:11Z","timestamp":1688110211000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/12\/3894\/5823296"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,4,21]]},"references-count":6,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2020,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa262","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/674036","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,6,15]]},"published":{"date-parts":[[2020,4,21]]}}}