{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T09:04:07Z","timestamp":1780045447179,"version":"3.53.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,12,6]],"date-time":"2016-12-06T00:00:00Z","timestamp":1480982400000},"content-version":"vor","delay-in-days":12,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["1425\/13 to EH, 317\/13 to RS, and 1313\/13 to IM"],"award-info":[{"award-number":["1425\/13 to EH, 317\/13 to RS, and 1313\/13 to IM"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011199","name":"European Research Council","doi-asserted-by":"publisher","award":["640384"],"award-info":[{"award-number":["640384"]}],"id":[{"id":"10.13039\/100011199","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Gene Regulation in Complex Human Disease","award":["41\/11"],"award-info":[{"award-number":["41\/11"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Plasmids and other mobile elements are central contributors to microbial evolution and genome innovation. Recently, they have been found to have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their characterization through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing. Here, we attempt to ameliorate this situation by introducing a new circular element assembly algorithm, leveraging assembly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assemble cyclic sequences likely to be plasmids, phages and other circular elements.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce Recycler, the first tool that can extract complete circular contigs from sequence data of isolate microbial genomes, plasmidome and metagenome sequence data. We show that Recycler greatly increases the number of true plasmids recovered relative to other approaches while remaining highly accurate. We demonstrate this trend via simulations of plasmidomes, comparisons of predictions with reference data for isolate samples, and assessments of annotation accuracy on metagenome data. In addition, we provide validation by DNA amplification of 77 plasmids predicted by Recycler from the different sequenced samples in which Recycler showed mean accuracy of 89% across all data types\u2014isolate, microbiome and plasmidome.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>Recycler is available at http:\/\/github.com\/Shamir-Lab\/Recycler<\/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\/btw651","type":"journal-article","created":{"date-parts":[[2016,11,9]],"date-time":"2016-11-09T23:07:35Z","timestamp":1478732855000},"page":"475-482","source":"Crossref","is-referenced-by-count":141,"title":["Recycler: an algorithm for detecting plasmids from\n                    <i>de novo<\/i>\n                    assembly graphs"],"prefix":"10.1093","volume":"33","author":[{"given":"Roye","family":"Rozov","sequence":"first","affiliation":[{"name":"Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aya","family":"Brown Kav","sequence":"additional","affiliation":[{"name":"The Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Bogumil","sequence":"additional","affiliation":[{"name":"The Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naama","family":"Shterzer","sequence":"additional","affiliation":[{"name":"The Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eran","family":"Halperin","sequence":"additional","affiliation":[{"name":"Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel"},{"name":"Molecular Microbiology and Biotechnology Department, Tel-Aviv University, Tel Aviv, Israel"},{"name":"International Computer Science Institute, Berkeley, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Itzhak","family":"Mizrahi","sequence":"additional","affiliation":[{"name":"The Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ron","family":"Shamir","sequence":"additional","affiliation":[{"name":"Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,11,24]]},"reference":[{"key":"2023020204411310500_btw651-B1","author":"Antipov","year":"2016"},{"key":"2023020204411310500_btw651-B2","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. 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