{"id":"https://openalex.org/W2774669565","doi":"https://doi.org/10.1186/s12859-017-1919-y","title":"CAMSA: a tool for comparative analysis and merging of scaffold assemblies","display_name":"CAMSA: a tool for comparative analysis and merging of scaffold assemblies","publication_year":2017,"publication_date":"2017-12-01","ids":{"openalex":"https://openalex.org/W2774669565","doi":"https://doi.org/10.1186/s12859-017-1919-y","mag":"2774669565","pmid":"https://pubmed.ncbi.nlm.nih.gov/29244014"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1919-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1919-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1919-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1919-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073871292","display_name":"Sergey Aganezov","orcid":"https://orcid.org/0000-0003-2458-8323"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sergey S. Aganezov","raw_affiliation_strings":["ITMO University, 49 Kronverksky Pr., St. Petersburg, 197101, Russia. aganezov@cs.princeton.edu","Princeton University, 35 Olden St., Princeton, 08450, NJ, USA. aganezov@cs.princeton.edu","Princeton University, 35 Olden St., Princeton, 08450, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ITMO University, 49 Kronverksky Pr., St. Petersburg, 197101, Russia. aganezov@cs.princeton.edu","institution_ids":[]},{"raw_affiliation_string":"Princeton University, 35 Olden St., Princeton, 08450, NJ, USA. aganezov@cs.princeton.edu","institution_ids":[]},{"raw_affiliation_string":"Princeton University, 35 Olden St., Princeton, 08450, NJ, USA","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012222528","display_name":"Max A. Alekseyev","orcid":"https://orcid.org/0000-0002-5140-8095"},"institutions":[{"id":"https://openalex.org/I865166595","display_name":"George Washington University Virginia Campus","ror":"https://ror.org/03ms79854","country_code":"US","type":"education","lineage":["https://openalex.org/I865166595"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Max A. Alekseyev","raw_affiliation_strings":["The George Washington University, 45085 University Dr., Suite 305, Ashburn, 20147, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The George Washington University, 45085 University Dr., Suite 305, Ashburn, 20147, VA, USA","institution_ids":["https://openalex.org/I865166595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5073871292"],"corresponding_institution_ids":["https://openalex.org/I20089843"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7851,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.72360569,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"18","issue":"S15","first_page":"496","last_page":"496"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4830000102519989,"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":0.4830000102519989,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.27399998903274536,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.0502999983727932,"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/scaffold","display_name":"Scaffold","score":0.8031121492385864},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.7702928781509399},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6875812411308289},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5704250335693359},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5360143184661865},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3572891354560852},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33945995569229126},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18248483538627625},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.145751953125},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12285348773002625}],"concepts":[{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.8031121492385864},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.7702928781509399},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6875812411308289},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5704250335693359},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5360143184661865},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3572891354560852},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33945995569229126},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18248483538627625},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.145751953125},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12285348773002625},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-017-1919-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1919-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1919-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29244014","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29244014","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:71793ec1284948ac8b54bcc23e3549dc","is_oa":true,"landing_page_url":"https://doaj.org/article/71793ec1284948ac8b54bcc23e3549dc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 18, Iss S15, Pp 41-50 (2017)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5731503","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5731503","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1919-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1919-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1919-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth","score":0.6100000143051147}],"awards":[{"id":"https://openalex.org/G5507455206","display_name":"CAREER: PRUGC---Phylogenetic Reconstructions with Unequal Gene Contents","funder_award_id":"1462107","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7470637954","display_name":null,"funder_award_id":"IIS-1462107","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2774669565.pdf","grobid_xml":"https://content.openalex.org/works/W2774669565.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W570339359","https://openalex.org/W1510244790","https://openalex.org/W1765935460","https://openalex.org/W1966822396","https://openalex.org/W1970995855","https://openalex.org/W2001914359","https://openalex.org/W2011246380","https://openalex.org/W2019063045","https://openalex.org/W2021920872","https://openalex.org/W2022986961","https://openalex.org/W2056227286","https://openalex.org/W2069531683","https://openalex.org/W2072841531","https://openalex.org/W2074104070","https://openalex.org/W2076163156","https://openalex.org/W2080090262","https://openalex.org/W2107282968","https://openalex.org/W2107772251","https://openalex.org/W2115501618","https://openalex.org/W2118970626","https://openalex.org/W2120902911","https://openalex.org/W2121832832","https://openalex.org/W2122546565","https://openalex.org/W2124827052","https://openalex.org/W2127768708","https://openalex.org/W2129744420","https://openalex.org/W2129933858","https://openalex.org/W2131852975","https://openalex.org/W2132022337","https://openalex.org/W2132787769","https://openalex.org/W2132842643","https://openalex.org/W2134675370","https://openalex.org/W2136104403","https://openalex.org/W2139118683","https://openalex.org/W2140059069","https://openalex.org/W2140947746","https://openalex.org/W2152554673","https://openalex.org/W2153218781","https://openalex.org/W2157068560","https://openalex.org/W2159675211","https://openalex.org/W2165795500","https://openalex.org/W2167757586","https://openalex.org/W2179127114","https://openalex.org/W2292368211","https://openalex.org/W2326939325","https://openalex.org/W2502621246","https://openalex.org/W2912500497","https://openalex.org/W2951239321","https://openalex.org/W3144688185","https://openalex.org/W4238387639"],"related_works":["https://openalex.org/W2081717811","https://openalex.org/W2695162732","https://openalex.org/W4234886518","https://openalex.org/W2884765235","https://openalex.org/W2351880312","https://openalex.org/W2794386548","https://openalex.org/W4381279187","https://openalex.org/W1992950355","https://openalex.org/W2013063066","https://openalex.org/W1841715584"],"abstract_inverted_index":{"BACKGROUND:":[0],"Despite":[1],"the":[2,12,39,53,138,156,160,177,210,215,222,236,264,272],"recent":[3],"progress":[4],"in":[5,18,169,212],"genome":[6,40,54],"sequencing":[7],"and":[8,36,61,79,91,115,144,230,245,252,270],"assembly,":[9,249],"many":[10],"of":[11,26,30,48,52,117,155,179,198,214,225,232,235,266,279],"currently":[13],"available":[14],"assembled":[15],"genomes":[16,24],"come":[17],"a":[19,27,46,151],"draft":[20,23,277],"form.":[21],"Such":[22],"consist":[25],"large":[28],"number":[29,47],"genomic":[31],"fragments":[32],"(scaffolds),":[33],"whose":[34],"positions":[35],"orientations":[37],"along":[38],"are":[41,187],"unknown.":[42],"While":[43],"there":[44,241],"exists":[45],"methods":[49,244,259],"for":[50,95,112,150,227,247,263,271],"reconstruction":[51],"from":[55],"its":[56],"scaffolds,":[57],"utilizing":[58],"various":[59],"computational":[60],"wet-lab":[62],"techniques,":[63],"they":[64],"often":[65],"can":[66,166],"produce":[67],"only":[68,163],"partial":[69],"error-prone":[70],"scaffold":[71,81,122,142,164,248,267],"assemblies.":[72,123,158],"It":[73],"therefore":[74],"becomes":[75],"important":[76],"to":[77,171],"compare":[78],"merge":[80],"assemblies":[82,197,234,255,278],"produced":[83,256],"by":[84,257],"different":[85,258],"methods,":[86],"thus":[87],"combining":[88],"their":[89,184],"advantages":[90],"highlighting":[92],"present":[93,109],"conflicts":[94],"further":[96],"investigation.":[97],"These":[98],"tasks":[99],"may":[100],"be":[101,167],"labor":[102],"intensive":[103],"if":[104],"performed":[105],"manually.":[106],"RESULTS:":[107],"We":[108],"CAMSA-a":[110],"tool":[111,125],"comparative":[113,133,153],"analysis":[114,154,231],"merging":[116,165],"two":[118],"or":[119,200],"more":[120],"given":[121,157],"The":[124],"(i)":[126],"creates":[127],"an":[128,147],"extensive":[129],"report":[130],"with":[131],"several":[132],"quality":[134,202],"metrics;":[135],"(ii)":[136],"constructs":[137],"most":[139],"confident":[140],"merged":[141,196],"assembly;":[143],"(iii)":[145],"provides":[146],"interactive":[148],"framework":[149],"visual":[152],"Among":[159],"CAMSA":[161,194,220],"features,":[162],"evaluated":[168],"comparison":[170,229],"existing":[172,204],"methods.":[173],"Namely,":[174],"it":[175],"resembles":[176],"functionality":[178],"assembly":[180,205,268],"reconciliation":[181,206],"tools,":[182],"although":[183],"primary":[185],"targets":[186],"somewhat":[188],"different.":[189],"Our":[190],"evaluations":[191],"show":[192],"that":[193],"produces":[195],"comparable":[199],"better":[201],"than":[203],"tools":[207,226],"while":[208],"being":[209],"fastest":[211],"terms":[213],"total":[216],"running":[217],"time.":[218],"CONCLUSIONS:":[219],"addresses":[221],"current":[223],"deficiency":[224],"automated":[228],"multiple":[233],"same":[237],"set":[238],"scaffolds.":[239],"Since":[240],"exist":[242],"numerous":[243],"techniques":[246],"identifying":[250],"similarities":[251],"dissimilarities":[253],"across":[254],"is":[260],"beneficial":[261],"both":[262],"developers":[265],"algorithms":[269],"researchers":[273],"focused":[274],"on":[275],"improving":[276],"specific":[280],"organisms.":[281]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}