{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T04:42:26Z","timestamp":1774672946003,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2017,1,27]],"date-time":"2017-01-27T00:00:00Z","timestamp":1485475200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"ELIXIR-ITA and BioForIU","award":["PONa3_00025"],"award-info":[{"award-number":["PONa3_00025"]}]},{"name":"Spanish Ministry of Economy and Competitiveness and European Regional Development","award":["PE - 2011 - 02346905"],"award-info":[{"award-number":["PE - 2011 - 02346905"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life domains (e.g. only bacteria). We present here MetaShot, a workflow for assessing the total microbiome composition from host-associated shotgun sequence data, and show its overall optimal accuracy performance by analyzing both simulated and real datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/bfosso\/MetaShot<\/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\/btx036","type":"journal-article","created":{"date-parts":[[2017,1,28]],"date-time":"2017-01-28T01:25:31Z","timestamp":1485566731000},"page":"1730-1732","source":"Crossref","is-referenced-by-count":22,"title":["MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data"],"prefix":"10.1093","volume":"33","author":[{"given":"B","family":"Fosso","sequence":"first","affiliation":[{"name":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy"}]},{"given":"M","family":"Santamaria","sequence":"additional","affiliation":[{"name":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy"}]},{"given":"M","family":"D\u2019Antonio","sequence":"additional","affiliation":[{"name":"CINECA, Rome, Italy"}]},{"given":"D","family":"Lovero","sequence":"additional","affiliation":[{"name":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy"}]},{"given":"G","family":"Corrado","sequence":"additional","affiliation":[{"name":"Department of Oncological Surgery, Gynecologic Oncology Unit, \u201cRegina Elena\u201d National Cancer Institute, Rome, Italy"}]},{"given":"E","family":"Vizza","sequence":"additional","affiliation":[{"name":"Department of Oncological Surgery, Gynecologic Oncology Unit, \u201cRegina Elena\u201d National Cancer Institute, Rome, Italy"}]},{"given":"N","family":"Passaro","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Neurosciences, Italian National Institute of Health, Rome, Italy"}]},{"given":"A R","family":"Garbuglia","sequence":"additional","affiliation":[{"name":"Lazzaro Spallanzani National Institute for Infectious Diseases, Rome, Italy"}]},{"given":"M R","family":"Capobianchi","sequence":"additional","affiliation":[{"name":"Lazzaro Spallanzani National Institute for Infectious Diseases, Rome, Italy"}]},{"given":"M","family":"Crescenzi","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Neurosciences, Italian National Institute of Health, Rome, Italy"}]},{"given":"G","family":"Valiente","sequence":"additional","affiliation":[{"name":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain"}]},{"given":"G","family":"Pesole","sequence":"additional","affiliation":[{"name":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy"},{"name":"Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari \u201cA. Moro\u201d, Bari, Italy"}]}],"member":"286","published-online":{"date-parts":[[2017,1,27]]},"reference":[{"key":"2023020205311699800_btx036-B1","doi-asserted-by":"crossref","first-page":"180.","DOI":"10.3389\/fonc.2013.00180","article-title":"Detection of Human Endogenous Retrovirus K (HERV-K) transcripts in human prostate cancer cell lines","volume":"3","author":"Agoni","year":"2013","journal-title":"Front. 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