{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:48Z","timestamp":1740185148863,"version":"3.37.3"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2020,4,24]],"date-time":"2020-04-24T00:00:00Z","timestamp":1587686400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Minist\u00e8re de la Recherche et de l\u2019Enseignement Sup\u00e9rieur"},{"name":"LabEx CALSIMLAB","award":["ANR-11-LABX-0037-01","ANR-11-IDEX-0004-02"],"award-info":[{"award-number":["ANR-11-LABX-0037-01","ANR-11-IDEX-0004-02"]}]},{"DOI":"10.13039\/501100004795","name":"Institut Universitaire de France","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004795","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The understanding of the ever-increasing number of metagenomic sequences accumulating in our databases demands for approaches that rapidly \u2018explore\u2019 the content of multiple and\/or large metagenomic datasets with respect to specific domain targets, avoiding full domain annotation and full assembly.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>S3A is a fast and accurate domain-targeted assembler designed for a rapid functional profiling. It is based on a novel construction and a fast traversal of the Overlap-Layout-Consensus graph, designed to reconstruct coding regions from domain annotated metagenomic sequence reads. S3A relies on high-quality domain annotation to efficiently assemble metagenomic sequences and on the design of a new confidence measure for a fast evaluation of overlapping reads. Its implementation is highly generic and can be applied to any arbitrary type of annotation. On simulated data, S3A achieves a level of accuracy similar to that of classical metagenomics assembly tools while permitting to conduct a faster and sensitive profiling on domains of interest. When studying a few dozens of functional domains\u2014a typical scenario\u2014S3A is up to an order of magnitude faster than general purpose metagenomic assemblers, thus enabling the analysis of a larger number of datasets in the same amount of time. S3A opens new avenues to the fast exploration of the rapidly increasing number of metagenomic datasets displaying an ever-increasing size.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>S3A is available at http:\/\/www.lcqb.upmc.fr\/S3A_ASSEMBLER\/.<\/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\/btaa272","type":"journal-article","created":{"date-parts":[[2020,4,17]],"date-time":"2020-04-17T11:13:55Z","timestamp":1587122035000},"page":"3975-3981","source":"Crossref","is-referenced-by-count":2,"title":["Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A"],"prefix":"10.1093","volume":"36","author":[{"given":"Laurent","family":"David","sequence":"first","affiliation":[{"name":"Sorbonne Universit\u00e9 , CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riccardo","family":"Vicedomini","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9 , CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238"},{"name":"Sorbonne Universit\u00e9 , CNRS, Institut des Sciences du Calcul et des Donn\u00e9es (ISCD)"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hugues","family":"Richard","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9 , CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238"},{"name":"Bioinformatics Unit (MF1), Robert Koch Institute , Berlin 13353, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandra","family":"Carbone","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9 , CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238"},{"name":"Institut Universitaire de France , Paris 75005, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,4,24]]},"reference":[{"key":"2023062300444019800_btaa272-B1","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/nrmicro1157","article-title":"Community genomics in microbial ecology and evolution","volume":"3","author":"Allen","year":"2005","journal-title":"Nat. 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