{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T21:57:18Z","timestamp":1776722238266,"version":"3.51.2"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2020,8,13]],"date-time":"2020-08-13T00:00:00Z","timestamp":1597276800000},"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\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["61972231"],"award-info":[{"award-number":["61972231"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["U1806205"],"award-info":[{"award-number":["U1806205"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Project of Joint Fund of Shandong Province","award":["ZR2019LZH007"],"award-info":[{"award-number":["ZR2019LZH007"]}]},{"name":"Shenzhen Basic Research Fund","award":["JCYJ20180507182818013"],"award-info":[{"award-number":["JCYJ20180507182818013"]}]},{"DOI":"10.13039\/100009108","name":"Shandong University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009108","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Center for High Performance Computing and System Simulation, Pilot National Laboratory for Marine Science and Technology"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Modern sequencing technologies continue to revolutionize many areas of biology and medicine. Since the generated datasets are error-prone, downstream applications usually require quality control methods to pre-process FASTQ files. However, existing tools for this task are currently not able to fully exploit the capabilities of computing platforms leading to slow runtimes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present RabbitQC, an extremely fast integrated quality control tool for FASTQ files, which can take full advantage of modern hardware. It includes a variety of operations and supports different sequencing technologies (Illumina, Oxford Nanopore and PacBio). RabbitQC achieves speedups between one and two orders-of-magnitude compared to other state-of-the-art tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>C++ sources and binaries are available at https:\/\/github.com\/ZekunYin\/RabbitQC.<\/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\/btaa719","type":"journal-article","created":{"date-parts":[[2020,8,8]],"date-time":"2020-08-08T11:21:42Z","timestamp":1596885702000},"page":"573-574","source":"Crossref","is-referenced-by-count":17,"title":["RabbitQC: high-speed scalable quality control for sequencing data"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6002-0028","authenticated-orcid":false,"given":"Zekun","family":"Yin","sequence":"first","affiliation":[{"name":"School of Software, Shandong University , Jinan, China"},{"name":"Shenzhen Research Institute of Shandong University , Shenzhen, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University , Jinan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meiyang","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University , Jinan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University , Jinan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Honglei","family":"Song","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University , Jinan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haidong","family":"Lan","sequence":"additional","affiliation":[{"name":"Tencent AI Lab , Shenzhen, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanjie","family":"Wei","sequence":"additional","affiliation":[{"name":"Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beifang","family":"Niu","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences , Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Institute for Computer Science, Johannes Gutenberg University , Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weiguo","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University , Jinan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,8,13]]},"reference":[{"key":"2023051706071499900_btaa719-B2","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2023051706071499900_btaa719-B3","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/s12859-017-1469-3","article-title":"AfterQC: automatic filtering, trimming, error removing and quality control for fastq data","volume":"18","author":"Chen","year":"2017","journal-title":"BMC 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