{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:15Z","timestamp":1740185115224,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2017,1,5]],"date-time":"2017-01-05T00:00:00Z","timestamp":1483574400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Johannes Gutenberg University Center for Computational Sciences"},{"DOI":"10.13039\/501100003558","name":"Ministry of Justice","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003558","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol. Cost-saving short (50-bp) single-end reads and Nextera\u00ae library preparation yield reliable results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Datasets, binaries and usage instructions are available under http:\/\/all-food-seq.sourceforge.net. Raw data is available at NCBI\u2019s SRA with accession number PRJNA271645.<\/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\/btw822","type":"journal-article","created":{"date-parts":[[2017,1,6]],"date-time":"2017-01-06T01:35:34Z","timestamp":1483666534000},"page":"1396-1398","source":"Crossref","is-referenced-by-count":10,"title":["AFS: identification and quantification of species composition by metagenomic sequencing"],"prefix":"10.1093","volume":"33","author":[{"given":"Yongchao","family":"Liu","sequence":"first","affiliation":[{"name":"Institute of Computer Science, Johannes Gutenberg University Mainz, Mainz, Germany"},{"name":"Georgia Institute of Technology, School of Computational Science and Engineering, Atlanta, GA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabian","family":"Ripp","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics, Johannes Gutenberg University Mainz, Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rene","family":"Koeppel","sequence":"additional","affiliation":[{"name":"Official Food Control Authority Canton Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanno","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics, Johannes Gutenberg University Mainz, Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S\u00f6ren Lukas","family":"Hellmann","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics, Johannes Gutenberg University Mainz, Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathias","family":"Weber","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics, Johannes Gutenberg University Mainz, Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher Felix","family":"Krombholz","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics, Johannes Gutenberg University Mainz, Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, Johannes Gutenberg University Mainz, Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Hankeln","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics, Johannes Gutenberg University Mainz, Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,1,5]]},"reference":[{"key":"2023020205021509400_btw822-B1","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1007\/s00217-010-1371-y","article-title":"Multiplex real-time PCR for the detection and quantification of DNA from beef, pork, horse and sheep","volume":"232","author":"Koeppel","year":"2011","journal-title":"Eur. Food Res. Technol"},{"key":"2023020205021509400_btw822-B2","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020205021509400_btw822-B3","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020205021509400_btw822-B4","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2164-15-639","article-title":"All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing","volume":"15","author":"Ripp","year":"2014","journal-title":"BMC Genomics"},{"key":"2023020205021509400_btw822-B5","doi-asserted-by":"crossref","first-page":"e83761.","DOI":"10.1371\/journal.pone.0083761","article-title":"A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures","volume":"8","author":"Tillmar","year":"2013","journal-title":"Plos One"},{"key":"2023020205021509400_btw822-B6","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\/33\/9\/1396\/49038600\/bioinformatics_33_9_1396.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/9\/1396\/49038600\/bioinformatics_33_9_1396.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T05:05:56Z","timestamp":1675314356000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/9\/1396\/2836026"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,1,5]]},"references-count":6,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2017,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw822","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2017,5,1]]},"published":{"date-parts":[[2017,1,5]]}}}