{"id":"https://openalex.org/W2511543798","doi":"https://doi.org/10.1186/s13029-016-0058-6","title":"cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing","display_name":"cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing","publication_year":2016,"publication_date":"2016-08-17","ids":{"openalex":"https://openalex.org/W2511543798","doi":"https://doi.org/10.1186/s13029-016-0058-6","mag":"2511543798","pmid":"https://pubmed.ncbi.nlm.nih.gov/27536334"},"language":"en","primary_location":{"id":"doi:10.1186/s13029-016-0058-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13029-016-0058-6","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/s13029-016-0058-6","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/s13029-016-0058-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010143923","display_name":"Toshiki Takeuchi","orcid":"https://orcid.org/0000-0002-3887-7452"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Toshiki Takeuchi","raw_affiliation_strings":["Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3887-7452","affiliations":[{"raw_affiliation_string":"Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041748597","display_name":"Atsuo Yamada","orcid":"https://orcid.org/0000-0002-7880-5701"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Atsuo Yamada","raw_affiliation_strings":["Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102962206","display_name":"Takashi Aoki","orcid":"https://orcid.org/0000-0001-8625-6151"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Takashi Aoki","raw_affiliation_strings":["Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050241636","display_name":"Kunihiro Nishimura","orcid":"https://orcid.org/0000-0002-0639-0949"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kunihiro Nishimura","raw_affiliation_strings":["Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5010143923"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6963,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.74556198,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"11","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8986999988555908,"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":0.8986999988555908,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.017100000753998756,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.005499999970197678,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6956912279129028},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5330167412757874},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4717976450920105},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3881445825099945},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38210543990135193},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09582206606864929},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08339786529541016}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6956912279129028},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5330167412757874},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4717976450920105},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3881445825099945},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38210543990135193},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09582206606864929},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08339786529541016}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13029-016-0058-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13029-016-0058-6","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/s13029-016-0058-6","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:27536334","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27536334","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4987990","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4987990","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":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13029-016-0058-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13029-016-0058-6","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/s13029-016-0058-6","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2511543798.pdf","grobid_xml":"https://content.openalex.org/works/W2511543798.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1496957882","https://openalex.org/W1990393483","https://openalex.org/W2056905592","https://openalex.org/W2070310827","https://openalex.org/W2100161431","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2109453587","https://openalex.org/W2124985265","https://openalex.org/W4253716618"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"BACKGROUND:":[0],"Next-generation":[1],"sequencing":[2,102],"can":[3,76,109,137,154],"determine":[4],"DNA":[5],"bases":[6],"and":[7,24,63,65,75,112,156,162,185],"the":[8,19,25,42,61,98,124,173],"results":[9],"of":[10,30,51,54,58,60,67,100],"sequence":[11],"alignments":[12],"are":[13],"generally":[14],"stored":[15],"in":[16,18,41,73,88,139,160,183],"files":[17,40,159],"Sequence":[20],"Alignment/Map":[21],"(SAM)":[22],"format":[23],"compressed":[26],"binary":[27],"version":[28],"(BAM)":[29],"it.":[31],"SAMtools":[32,45,80],"is":[33,71,116,171,181],"a":[34,104,140],"typical":[35],"tool":[36],"for":[37,91],"dealing":[38],"with":[39,150,169,176],"SAM/BAM":[43,134,158],"format.":[44],"has":[46,186],"various":[47],"functions,":[48],"including":[49],"detection":[50],"variants,":[52],"visualization":[53],"alignments,":[55],"indexing,":[56],"extraction":[57],"parts":[59],"data":[62],"loci,":[64],"conversion":[66],"file":[68],"formats.":[69],"It":[70],"written":[72,182],"C":[74],"execute":[77],"fast.":[78],"However,":[79],"requires":[81],"an":[82],"additional":[83],"implementation":[84],"to":[85,132],"be":[86],"used":[87],"parallel":[89,130,161],"with,":[90],"example,":[92],"OpenMP":[93],"(Open":[94],"Multi-Processing)":[95],"libraries.":[96],"For":[97],"accumulation":[99],"next-generation":[101],"data,":[103],"simple":[105],"parallelization":[106],"program,":[107],"which":[108,128],"support":[110],"cloud":[111],"PC":[113],"cluster":[114],"environments,":[115],"required.":[117],"RESULTS:":[118],"We":[119],"have":[120],"developed":[121],"cljam":[122,170,179],"using":[123],"Clojure":[125,184],"programming":[126],"language,":[127],"simplifies":[129],"programming,":[131],"handle":[133],"data.":[135],"Cljam":[136,153],"run":[138],"Java":[141],"runtime":[142],"environment":[143],"(e.g.,":[144],"Windows,":[145],"Linux,":[146],"Mac":[147],"OS":[148],"X)":[149],"Clojure.":[151],"CONCLUSIONS:":[152],"process":[155],"analyze":[157],"at":[163],"high":[164],"speed.":[165],"The":[166,178],"execution":[167],"time":[168],"almost":[172],"same":[174],"as":[175],"SAMtools.":[177],"code":[180],"fewer":[187],"lines":[188],"than":[189],"other":[190],"similar":[191],"tools.":[192]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
