{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:15Z","timestamp":1772138055479,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"Supplement_2","license":[{"start":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T00:00:00Z","timestamp":1661990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"United State\u2014Israel Binational Science Foundation","award":["ECCB2022"],"award-info":[{"award-number":["ECCB2022"]}]},{"name":"United State\u2014Israel Binational Science Foundation","award":["2016694"],"award-info":[{"award-number":["2016694"]}]},{"name":"United States National Science Foundation"},{"name":"Edmond J. Safra Center for Bioinformatics at Tel-Aviv University"},{"DOI":"10.13039\/501100009328","name":"Planning and Budgeting Committee","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009328","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005385","name":"Council for Higher Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005385","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Bacteriophages and plasmids usually coexist with their host bacteria in microbial communities and play important roles in microbial evolution. Accurately identifying sequence contigs as phages, plasmids and bacterial chromosomes in mixed metagenomic assemblies is critical for further unraveling their functions. Many classification tools have been developed for identifying either phages or plasmids in metagenomic assemblies. However, only two classifiers, PPR-Meta and viralVerify, were proposed to simultaneously identify phages and plasmids in mixed metagenomic assemblies. Due to the very high fraction of chromosome contigs in the assemblies, both tools achieve high precision in the classification of chromosomes but perform poorly in classifying phages and plasmids. Short contigs in these assemblies are often wrongly classified or classified as uncertain.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we present 3CAC, a new three-class classifier that improves the precision of phage and plasmid classification. 3CAC starts with an initial three-class classification generated by existing classifiers and improves the classification of short contigs and contigs with low confidence classification by using proximity in the assembly graph. Evaluation on simulated metagenomes and on real human gut microbiome samples showed that 3CAC outperformed PPR-Meta and viralVerify in both precision and recall, and increased F1-score by 10\u201360 percentage points.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The 3CAC software is available on https:\/\/github.com\/Shamir-Lab\/3CAC.<\/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\/btac468","type":"journal-article","created":{"date-parts":[[2022,8,24]],"date-time":"2022-08-24T10:20:18Z","timestamp":1661336418000},"page":"ii56-ii61","source":"Crossref","is-referenced-by-count":5,"title":["3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs"],"prefix":"10.1093","volume":"38","author":[{"given":"Lianrong","family":"Pu","sequence":"first","affiliation":[{"name":"The Blavatnik School of Computer Science, Tel Aviv University , Tel Aviv, 69978, Israel"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1889-9870","authenticated-orcid":false,"given":"Ron","family":"Shamir","sequence":"additional","affiliation":[{"name":"The Blavatnik School of Computer Science, Tel Aviv University , Tel Aviv, 69978, Israel"}]}],"member":"286","published-online":{"date-parts":[[2022,9,18]]},"reference":[{"key":"2023041408002293700_","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.241299.118","article-title":"Plasmid detection and assembly in genomic and metagenomic data sets","volume":"29","author":"Antipov","year":"2019","journal-title":"Genome Res"},{"key":"2023041408002293700_","doi-asserted-by":"crossref","first-page":"4126","DOI":"10.1093\/bioinformatics\/btaa490","article-title":"Metaviral SPAdes: assembly of viruses from metagenomic data","volume":"36","author":"Antipov","year":"2020","journal-title":"Bioinformatics"},{"key":"2023041408002293700_","doi-asserted-by":"crossref","first-page":"e000128","DOI":"10.1099\/mgen.0.000128","article-title":"On the (im) possibility of reconstructing plasmids from whole-genome short-read sequencing data","volume":"3","author":"Arredondo-Alonso","year":"2017","journal-title":"Microbial Genomics"},{"key":"2023041408002293700_","doi-asserted-by":"crossref","first-page":"e121","DOI":"10.1093\/nar\/gkaa856","article-title":"Seeker: alignment-free identification of bacteriophage genomes by deep learning","volume":"48","author":"Auslander","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023041408002293700_","doi-asserted-by":"crossref","first-page":"1568","DOI":"10.1038\/s41396-018-0081-5","article-title":"Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities","volume":"12","author":"Barnum","year":"2018","journal-title":"ISME J"},{"key":"2023041408002293700_","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/s41587-021-01130-z","article-title":"Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities","volume":"40","author":"Bickhart","year":"2022","journal-title":"Nature Biotechnol"},{"key":"2023041408002293700_","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1016\/j.tim.2019.02.008","article-title":"Bacteriophages as environmental reservoirs of antibiotic resistance","volume":"27","author":"Calero-C\u00e1ceres","year":"2019","journal-title":"Trends Microbiol"},{"key":"2023041408002293700_","doi-asserted-by":"crossref","first-page":"giz066","DOI":"10.1093\/gigascience\/giz066","article-title":"PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning","volume":"8","author":"Fang","year":"2019","journal-title":"GigaScience"},{"key":"2023041408002293700_","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nrmicro1235","article-title":"Mobile genetic elements: the agents of open source evolution","volume":"3","author":"Frost","year":"2005","journal-title":"Nat. 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