{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T04:30:53Z","timestamp":1774672253730,"version":"3.50.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources.<\/jats:p>\n               <jats:p>Results: We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly.<\/jats:p>\n               <jats:p>Availability: Bambus 2 is open source and available from http:\/\/amos.sf.net.<\/jats:p>\n               <jats:p>Contact: \u00a0mpop@umiacs.umd.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr520","type":"journal-article","created":{"date-parts":[[2011,9,17]],"date-time":"2011-09-17T03:20:48Z","timestamp":1316229648000},"page":"2964-2971","source":"Crossref","is-referenced-by-count":116,"title":["Bambus 2: scaffolding metagenomes"],"prefix":"10.1093","volume":"27","author":[{"given":"Sergey","family":"Koren","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, University of Maryland, College Park, MD 20742, 2J. Craig Venter Institute, Rockville, MD 20850 and 3Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA"},{"name":"1 Department of Computer Science, University of Maryland, College Park, MD 20742, 2J. Craig Venter Institute, Rockville, MD 20850 and 3Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA"},{"name":"1 Department of Computer Science, University of Maryland, College Park, MD 20742, 2J. Craig Venter Institute, Rockville, MD 20850 and 3Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA"}]},{"given":"Todd J.","family":"Treangen","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, University of Maryland, College Park, MD 20742, 2J. Craig Venter Institute, Rockville, MD 20850 and 3Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA"}]},{"given":"Mihai","family":"Pop","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, University of Maryland, College Park, MD 20742, 2J. Craig Venter Institute, Rockville, MD 20850 and 3Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA"},{"name":"1 Department of Computer Science, University of Maryland, College Park, MD 20742, 2J. Craig Venter Institute, Rockville, MD 20850 and 3Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,9,16]]},"reference":[{"key":"2023012511340083200_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. 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