{"id":"https://openalex.org/W2140059069","doi":"https://doi.org/10.1093/bioinformatics/btr520","title":"Bambus 2: scaffolding metagenomes","display_name":"Bambus 2: scaffolding metagenomes","publication_year":2011,"publication_date":"2011-09-16","ids":{"openalex":"https://openalex.org/W2140059069","doi":"https://doi.org/10.1093/bioinformatics/btr520","mag":"2140059069","pmid":"https://pubmed.ncbi.nlm.nih.gov/21926123"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr520","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr520","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/2964/48864148/bioinformatics_27_21_2964.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/2964/48864148/bioinformatics_27_21_2964.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042603880","display_name":"Sergey Koren","orcid":"https://orcid.org/0000-0002-1472-8962"},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergey Koren","raw_affiliation_strings":["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"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I1301553790","https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054369332","display_name":"Todd J. Treangen","orcid":"https://orcid.org/0000-0002-3760-564X"},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Todd J. Treangen","raw_affiliation_strings":["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"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I1301553790","https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064979917","display_name":"Mihai Pop","orcid":"https://orcid.org/0000-0001-9617-5304"},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mihai Pop","raw_affiliation_strings":["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"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I1301553790","https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5064979917"],"corresponding_institution_ids":["https://openalex.org/I1301553790","https://openalex.org/I66946132"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":6.3565,"has_fulltext":true,"cited_by_count":139,"citation_normalized_percentile":{"value":0.97602812,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"27","issue":"21","first_page":"2964","last_page":"2971"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8944000005722046,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8944000005722046,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.024000000208616257,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.008200000040233135,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.8903543949127197},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6140168309211731},{"id":"https://openalex.org/keywords/joins","display_name":"Joins","score":0.5723402500152588},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5696747303009033},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49371060729026794},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.440354585647583},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3951519727706909},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14808595180511475},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11815813183784485},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10529008507728577}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8903543949127197},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6140168309211731},{"id":"https://openalex.org/C2778692605","wikidata":"https://www.wikidata.org/wiki/Q4041866","display_name":"Joins","level":2,"score":0.5723402500152588},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5696747303009033},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49371060729026794},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.440354585647583},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3951519727706909},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14808595180511475},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11815813183784485},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10529008507728577}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr520","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr520","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/2964/48864148/bioinformatics_27_21_2964.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21926123","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21926123","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Evaluation Study"},{"id":"pmh:oai:pubmedcentral.nih.gov:3198580","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3198580","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/21/2964","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/21/2964","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr520","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr520","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/2964/48864148/bioinformatics_27_21_2964.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G164339318","display_name":"Assembly and analysis software for exploring the human microbiome","funder_award_id":"5r01hg004885-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1979396419","display_name":null,"funder_award_id":"R01 HG004885","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8984482210","display_name":"III-CXT-Small: Graphs to Diversity: extracting genomic variation from sequence graphs","funder_award_id":"0812111","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2140059069.pdf","grobid_xml":"https://content.openalex.org/works/W2140059069.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1635391495","https://openalex.org/W1791999417","https://openalex.org/W1850079471","https://openalex.org/W1939138306","https://openalex.org/W1969346416","https://openalex.org/W1970995855","https://openalex.org/W1971937094","https://openalex.org/W1972254009","https://openalex.org/W1982827785","https://openalex.org/W1984236772","https://openalex.org/W2001914359","https://openalex.org/W2003574450","https://openalex.org/W2020053713","https://openalex.org/W2032230795","https://openalex.org/W2033531015","https://openalex.org/W2042008515","https://openalex.org/W2045765967","https://openalex.org/W2047927409","https://openalex.org/W2048818637","https://openalex.org/W2055043387","https://openalex.org/W2056944867","https://openalex.org/W2058370375","https://openalex.org/W2078331392","https://openalex.org/W2093830129","https://openalex.org/W2096634299","https://openalex.org/W2106882534","https://openalex.org/W2107282968","https://openalex.org/W2113601822","https://openalex.org/W2113915152","https://openalex.org/W2124637227","https://openalex.org/W2125826054","https://openalex.org/W2128114769","https://openalex.org/W2132415967","https://openalex.org/W2133790733","https://openalex.org/W2139183861","https://openalex.org/W2139884694","https://openalex.org/W2142749416","https://openalex.org/W2143191932","https://openalex.org/W2149573313","https://openalex.org/W2151674273","https://openalex.org/W2154915161","https://openalex.org/W2160053034","https://openalex.org/W2160969485","https://openalex.org/W2161546116","https://openalex.org/W2166267493","https://openalex.org/W2171531867","https://openalex.org/W2477408078","https://openalex.org/W2905576637","https://openalex.org/W4238387639"],"related_works":["https://openalex.org/W2210738511","https://openalex.org/W2474302342","https://openalex.org/W1910109602","https://openalex.org/W4297131566","https://openalex.org/W2017364432","https://openalex.org/W2080583581","https://openalex.org/W3037682416","https://openalex.org/W3195915274","https://openalex.org/W3158976456","https://openalex.org/W4285082713"],"abstract_inverted_index":{"MOTIVATION:":[0],"Sequencing":[1],"projects":[2],"increasingly":[3],"target":[4],"samples":[5],"from":[6,45,154],"non-clonal":[7,46],"sources.":[8,47],"In":[9,120],"particular,":[10],"metagenomics":[11],"has":[12],"enabled":[13],"scientists":[14],"to":[15,17,40,56,86,96],"begin":[16],"characterize":[18],"the":[19,60,107,123],"structure":[20],"of":[21,59,72],"microbial":[22],"communities.":[23],"The":[24],"software":[25,95],"tools":[26],"developed":[27],"for":[28,34,76],"assembling":[29],"and":[30,80,101,152],"analyzing":[31,64],"sequencing":[32],"data":[33,43,161],"clonal":[35],"organisms":[36,131],"are,":[37],"however,":[38],"unable":[39],"adequately":[41],"process":[42],"derived":[44],"RESULTS:":[48],"We":[49,92,104],"present":[50],"a":[51,70,73,139],"new":[52],"scaffolder,":[53],"Bambus":[54,136,147],"2,":[55],"address":[57],"some":[58],"challenges":[61],"encountered":[62],"when":[63],"metagenomes.":[65],"Our":[66],"approach":[67],"relies":[68],"on":[69],"combination":[71],"novel":[74],"method":[75],"detecting":[77],"genomic":[78,90],"repeats":[79],"algorithms":[81,110],"that":[82,106],"analyze":[83],"assembly":[84],"graphs":[85],"identify":[87],"biologically":[88],"meaningful":[89],"variants.":[91],"compare":[93],"our":[94],"current":[97,115],"assemblers":[98],"using":[99],"simulated":[100],"real":[102],"data.":[103],"demonstrate":[105],"repeat":[108],"detection":[109],"have":[111],"higher":[112],"sensitivity":[113],"than":[114],"approaches":[116],"without":[117],"sacrificing":[118],"specificity.":[119],"metagenomic":[121,144],"datasets,":[122],"scaffolder":[124],"avoids":[125],"false":[126],"joins":[127],"between":[128],"distantly":[129],"related":[130],"while":[132],"obtaining":[133],"long-range":[134],"contiguity.":[135],"2":[137,148],"represents":[138],"first":[140],"step":[141],"toward":[142],"automated":[143],"assembly.":[145],"AVAILABILITY:":[146],"is":[149],"open":[150],"source":[151],"available":[153,163],"http://amos.sf.net.":[155],"CONTACT:":[156],"mpop@umiacs.umd.edu.":[157],"SUPPLEMENTARY":[158],"INFORMATION:":[159],"Supplementary":[160],"are":[162],"at":[164],"Bioinformatics":[165],"online.":[166]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":17},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":17}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
