{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T13:52:43Z","timestamp":1762005163496,"version":"build-2065373602"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2018,6,1]],"date-time":"2018-06-01T00:00:00Z","timestamp":1527811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"German Federal Ministry of Health","award":["2515NIK043"],"award-info":[{"award-number":["2515NIK043"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>In metagenomics, Kraken is one of the most widely used tools due to its robustness and speed. Yet, the overall turnaround time of metagenomic analysis is hampered by the sequential paradigm of wet and dry lab. In urgent experiments, it can be crucial to gain a timely insight into a dataset.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we present LiveKraken, a real-time read classification tool based on the core algorithm of Kraken. LiveKraken uses streams of raw data from Illumina sequencers to classify reads taxonomically. This way, we are able to produce results identical to those of Kraken the moment the sequencer finishes. We are furthermore able to provide comparable results in early stages of a sequencing run, allowing saving up to a week of sequencing time on an Illumina HiSeq in High Throughput Mode. While the number of classified reads grows over time, false classifications appear in negligible numbers and proportions of identified taxa are only affected to a minor extent.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>LiveKraken is available at https:\/\/gitlab.com\/rki_bioinformatics\/LiveKraken.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty433","type":"journal-article","created":{"date-parts":[[2018,5,30]],"date-time":"2018-05-30T11:20:10Z","timestamp":1527679210000},"page":"3750-3752","source":"Crossref","is-referenced-by-count":24,"title":["LiveKraken\u2013\u2013real-time metagenomic classification of illumina data"],"prefix":"10.1093","volume":"34","author":[{"given":"Simon H","family":"Tausch","sequence":"first","affiliation":[{"name":"Bioinformatics Unit (MF1)"},{"name":"Centre for Biological Threats and Special Pathogens (ZBS1), Robert Koch Institute, Berlin, Germany"}]},{"given":"Benjamin","family":"Strauch","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit (MF1)"}]},{"given":"Andreas","family":"Andrusch","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit (MF1)"},{"name":"Centre for Biological Threats and Special Pathogens (ZBS1), Robert Koch Institute, Berlin, Germany"}]},{"given":"Tobias P","family":"Loka","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit (MF1)"}]},{"given":"Martin S","family":"Lindner","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit (MF1)"}]},{"given":"Andreas","family":"Nitsche","sequence":"additional","affiliation":[{"name":"Centre for Biological Threats and Special Pathogens (ZBS1), Robert Koch Institute, Berlin, Germany"}]},{"given":"Bernhard Y","family":"Renard","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit (MF1)"}]}],"member":"286","published-online":{"date-parts":[[2018,6,1]]},"reference":[{"key":"2023012712444717500_bty433-B1","article-title":"Bioconda: a sustainable and comprehensive software distribution for the life sciences","author":"Gr\u00fcning","year":"2017","journal-title":"bioRxiv"},{"key":"2023012712444717500_bty433-B2","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1093\/bioinformatics\/btw659","article-title":"HiLive: real-time mapping of illumina reads while sequencing","volume":"33","author":"Lindner","year":"2017","journal-title":"Bioinformatics"},{"key":"2023012712444717500_bty433-B3","doi-asserted-by":"crossref","first-page":"2317","DOI":"10.1101\/gr.096651.109","article-title":"The NIH human microbiome project","volume":"19","author":"NIH HMP Working Group","year":"2009","journal-title":"Genome Res"},{"key":"2023012712444717500_bty433-B4","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O\u2019Leary","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712444717500_bty433-B5","doi-asserted-by":"crossref","first-page":"R46.","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/21\/3750\/48921457\/bioinformatics_34_21_3750.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/21\/3750\/48921457\/bioinformatics_34_21_3750.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,2]],"date-time":"2023-09-02T22:06:04Z","timestamp":1693692364000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/21\/3750\/5026657"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,1]]},"references-count":5,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2018,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty433","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,11,1]]},"published":{"date-parts":[[2018,6,1]]}}}