{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:40Z","timestamp":1740185140779,"version":"3.37.3"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2022,3,25]],"date-time":"2022-03-25T00:00:00Z","timestamp":1648166400000},"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":["62102231","61972231"],"award-info":[{"award-number":["62102231","61972231"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen Basic Research Fund","award":["JCYJ20180507182818013"],"award-info":[{"award-number":["JCYJ20180507182818013"]}]},{"name":"Key Project of Joint Fund of Shandong Province","award":["ZR2019LZH007"],"award-info":[{"award-number":["ZR2019LZH007"]}]},{"DOI":"10.13039\/501100007129","name":"Shandong Provincial Natural Science Foundation","doi-asserted-by":"publisher","award":["ZR2021QF089"],"award-info":[{"award-number":["ZR2021QF089"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"publisher"}]},{"name":"PPP project from CSC and DAAD"},{"name":"Engineering Research Center of Digital Media Technology, Ministry of Education"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Detection and identification of viruses and microorganisms in sequencing data plays an important role in pathogen diagnosis and research. However, existing tools for this problem often suffer from high runtimes and memory consumption.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present RabbitV, a tool for rapid detection of viruses and microorganisms in Illumina sequencing datasets based on fast identification of unique k-mers. It can exploit the power of modern multi-core CPUs by using multi-threading, vectorization and fast data parsing. Experiments show that RabbitV outperforms fastv by a factor of at least 42.5 and 14.4 in unique k-mer generation (RabbitUniq) and pathogen identification (RabbitV), respectively. Furthermore, RabbitV is able to detect COVID-19 from 40 samples of sequencing data (255\u2009GB in FASTQ format) in only 320\u2009s.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>RabbitUniq and RabbitV are available at https:\/\/github.com\/RabbitBio\/RabbitUniq and https:\/\/github.com\/RabbitBio\/RabbitV.<\/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\/btac187","type":"journal-article","created":{"date-parts":[[2022,3,24]],"date-time":"2022-03-24T21:52:41Z","timestamp":1648158761000},"page":"2932-2933","source":"Crossref","is-referenced-by-count":2,"title":["RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9548-5239","authenticated-orcid":false,"given":"Hao","family":"Zhang","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":"Qixin","family":"Chang","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University , Jinan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6002-0028","authenticated-orcid":false,"given":"Zekun","family":"Yin","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University , Jinan, China"},{"name":"Shenzhen Research Institute of Shandong University , Shenzhen, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0370-2222","authenticated-orcid":false,"given":"Xiaoming","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University , Jinan, China"},{"name":"Shenzhen Research Institute of Shandong University , 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":"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":[[2022,3,25]]},"reference":[{"key":"2023020109102586700_btac187-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-018-1568-0","article-title":"KrakenUniq: confident and fast metagenomics classification using unique k-mer counts","volume":"19","author":"Breitwieser","year":"2018","journal-title":"Genome Biol"},{"key":"2023020109102586700_btac187-B2","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1093\/bib\/bbaa231","article-title":"A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data","volume":"22","author":"Chen","year":"2021","journal-title":"Brief. 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