{"id":"https://openalex.org/W2128793361","doi":"https://doi.org/10.1093/bioinformatics/btp533","title":"Updates to the RMAP short-read mapping software","display_name":"Updates to the RMAP short-read mapping software","publication_year":2009,"publication_date":"2009-09-07","ids":{"openalex":"https://openalex.org/W2128793361","doi":"https://doi.org/10.1093/bioinformatics/btp533","mag":"2128793361","pmid":"https://pubmed.ncbi.nlm.nih.gov/19736251"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp533","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp533","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/21/2841/48997932/bioinformatics_25_21_2841.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/21/2841/48997932/bioinformatics_25_21_2841.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065682481","display_name":"Andrew D. Smith","orcid":"https://orcid.org/0000-0002-3337-1970"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrew D. Smith","raw_affiliation_strings":["1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053166972","display_name":"Wen\u2010Yu Chung","orcid":"https://orcid.org/0000-0003-3746-7301"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wen-Yu Chung","raw_affiliation_strings":["1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001669149","display_name":"Emily Hodges","orcid":"https://orcid.org/0000-0001-6513-610X"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily Hodges","raw_affiliation_strings":["1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112376231","display_name":"Jude Kendall","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jude Kendall","raw_affiliation_strings":["1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000505375","display_name":"Greg Hannon","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Greg Hannon","raw_affiliation_strings":["1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025053302","display_name":"James Hicks","orcid":"https://orcid.org/0000-0001-5353-4338"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Hicks","raw_affiliation_strings":["1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031286769","display_name":"Zhenyu Xuan","orcid":"https://orcid.org/0000-0001-9344-8493"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhenyu Xuan","raw_affiliation_strings":["1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522","https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103076277","display_name":"Michael Q. Zhang","orcid":"https://orcid.org/0000-0002-7408-1830"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael Q. Zhang","raw_affiliation_strings":["1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Molecular and Computational Biology, University of Southern California, Los Angeles, CA and 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522","https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5065682481","https://openalex.org/A5103076277"],"corresponding_institution_ids":["https://openalex.org/I1174212","https://openalex.org/I2750212522"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.0205,"has_fulltext":true,"cited_by_count":166,"citation_normalized_percentile":{"value":0.97823386,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"25","issue":"21","first_page":"2841","last_page":"2842"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.10899999737739563,"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":0.10899999737739563,"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/T11212","display_name":"Cultural Heritage Materials Analysis","score":0.029600000008940697,"subfield":{"id":"https://openalex.org/subfields/1204","display_name":"Archeology"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.02539999969303608,"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":0.7369509339332581},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6646727323532104},{"id":"https://openalex.org/keywords/os-x","display_name":"OS X","score":0.6393269300460815},{"id":"https://openalex.org/keywords/quality-score","display_name":"Quality Score","score":0.5279095768928528},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3690541386604309},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1918841302394867}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7369509339332581},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6646727323532104},{"id":"https://openalex.org/C515153823","wikidata":"https://www.wikidata.org/wiki/Q14116","display_name":"OS X","level":3,"score":0.6393269300460815},{"id":"https://openalex.org/C2779346075","wikidata":"https://www.wikidata.org/wiki/Q7268763","display_name":"Quality Score","level":3,"score":0.5279095768928528},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3690541386604309},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1918841302394867},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"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":"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btp533","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp533","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/21/2841/48997932/bioinformatics_25_21_2841.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19736251","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19736251","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":null},{"id":"pmh:oai:europepmc.org:1800553","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2895571","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:repository.cshl.edu:27476","is_oa":false,"landing_page_url":"https://repository.cshl.edu/id/eprint/27476/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Paper"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.483.4463","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.483.4463","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2009/09/07/bioinformatics.btp533.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp533","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp533","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/21/2841/48997932/bioinformatics_25_21_2841.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5400000214576721,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1007191511","display_name":null,"funder_award_id":"U01 ES017166","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G1998692746","display_name":null,"funder_award_id":"ES017166","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3049216827","display_name":null,"funder_award_id":"U01 ES017166","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6700237144","display_name":null,"funder_award_id":"T32 CA00917631","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G789504050","display_name":null,"funder_award_id":"P01 CA013106","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320306260","display_name":"Breast Cancer Research Foundation","ror":"https://ror.org/0348ff195"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128793361.pdf","grobid_xml":"https://content.openalex.org/works/W2128793361.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1501132557","https://openalex.org/W1987426253","https://openalex.org/W2052890777","https://openalex.org/W2072193858","https://openalex.org/W2112113834","https://openalex.org/W2121762798","https://openalex.org/W2124985265","https://openalex.org/W2139760555","https://openalex.org/W2143124024"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W642521392","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W599814909","https://openalex.org/W2466726934","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W145675224","https://openalex.org/W2128793361"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"We":[2,250],"report":[3,251],"on":[4,89,231,294],"a":[5,147,289],"major":[6,254],"new":[7,223],"version":[8],"of":[9,50,110,127,134,201,225,235,243,297,336,351],"the":[10,35,82,111,119,132,139,164,232,252,271,295,317,337],"RMAP":[11,36,99,128,263,287,304,338],"software":[12,37,80,85,339],"for":[13,41,70,115,343,357],"mapping":[14,42,45,55,58,116,140,168,216,237,245,344,355,359,362],"reads":[15,117,268,298,318,360],"from":[16,118],"short-read":[17,226],"sequencing":[18,122,227],"technology.":[19,123],"General":[20],"improvements":[21,195],"to":[22,130,205,215,256,266,305],"accuracy":[23],"and":[24,57,74,91,155,199,269,279,361],"space":[25],"requirements":[26,327],"are":[27,39,68,75],"included,":[28],"along":[29],"with":[30,144,194,312,322],"novel":[31],"functionality.":[32],"Included":[33,332],"in":[34,65,196,240,262,309,325,333],"package":[38,340],"tools":[40,246],"paired-end":[43,207,345],"reads,":[44,346],"using":[46],"more":[47,348],"sophisticated":[48,349],"use":[49,133,350],"quality":[51,135,148,157,352],"scores,":[52,353],"collecting":[53,354],"ambiguous":[54],"locations":[56,356],"bisulfite-treated":[59,363],"reads.":[60,364],"Availability:":[61],"The":[62,84,98,258],"applications":[63,224],"described":[64],"this":[66,334],"note":[67],"available":[69,113],"download":[71],"at":[72],"http://www.cmb.usc.edu/people/andrewds/rmap":[73],"distributed":[76],"as":[77,108],"Open":[78],"Source":[79],"under":[81],"GPLv3.0.":[83],"has":[86,283,288],"been":[87,277,284],"tested":[88],"Linux":[90],"OS":[92],"X":[93],"platforms.":[94],"Contact:":[95],"andrewds@usc.edu;":[96],"mzhang@cshl.edu":[97],"algorithm":[100,169],"was":[101,129],"introduced":[102],"by":[103,163],"(Smith":[104],"et":[105,173,177,181,185,191],"al.,":[106,174,178,182,186,192],"2008)":[107],"one":[109],"earliest":[112],"programs":[114],"Illumina":[120],"second-generation":[121],"One":[124],"important":[125],"contribution":[126],"incorporate":[131],"scores":[136],"directly":[137],"into":[138],"process:":[141],"read":[142,236],"positions":[143],"too":[145],"low":[146],"score":[149,158],"were":[150],"not":[151],"considered":[152],"while":[153],"mapping,":[154],"that":[156,292],"cutoff":[159],"could":[160],"be":[161,306],"adjusted":[162],"user.":[165],"Subsequently,":[166],"numerous":[167],"have":[170,219,276],"appeared":[171],"(Langmead":[172],"2009;":[175,189],"Li,H.":[176],"2008;":[179,183,187],"Li,R.":[180],"Lin":[184],"Schatz,":[188],"Yanovsky":[190],"2008),":[193],"both":[197],"efficiency":[198],"breadth":[200],"functionality":[202,282,342],"(e.g.":[203],"ability":[204],"map":[206],"reads;":[208],"integrated":[209],"SNP":[210],"calling).":[211],"Investigators":[212],"requiring":[213],"solutions":[214],"problems":[217],"now":[218],"many":[220,229],"options.":[221],"As":[222],"emerge,":[228],"variations":[230],"analysis":[233],"task":[234],"emerge.":[238],"Diversity":[239],"performance":[241],"characteristics":[242],"existing":[244],"becomes":[247],"potentially":[248],"valuable.":[249],"first":[253],"update":[255],"RMAP.":[257],"basic":[259],"algorithmic":[260],"framework":[261],"is":[264,341],"still":[265],"preprocess":[267],"scan":[270],"genome,":[272],"but":[273],"several":[274],"modifications":[275],"made":[278],"much":[280],"additional":[281],"included.":[285],"Importantly,":[286],"memory":[290,326],"footprint":[291],"depends":[293],"number":[296],"being":[299],"mapped.":[300],"This":[301],"feature":[302],"allows":[303,319],"used":[307],"effectively":[308],"cluster":[310],"environments":[311],"commodity":[313],"nodes,":[314],"because":[315],"partitioning":[316],"natural":[320],"parallelizations":[321],"linear":[323],"reduction":[324],"per":[328],"processor":[329],"core":[330],"used.":[331],"release":[335],"making":[347],"ambiguously":[358]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":20},{"year":2014,"cited_by_count":22},{"year":2013,"cited_by_count":14},{"year":2012,"cited_by_count":25}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
