{"id":"https://openalex.org/W2153805608","doi":"https://doi.org/10.1093/bioinformatics/btr477","title":"Comparative analysis of algorithms for next-generation sequencing read alignment","display_name":"Comparative analysis of algorithms for next-generation sequencing read alignment","publication_year":2011,"publication_date":"2011-08-19","ids":{"openalex":"https://openalex.org/W2153805608","doi":"https://doi.org/10.1093/bioinformatics/btr477","mag":"2153805608","pmid":"https://pubmed.ncbi.nlm.nih.gov/21856737"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr477","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr477","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/20/2790/48872412/bioinformatics_27_20_2790.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/27/20/2790/48872412/bioinformatics_27_20_2790.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091838807","display_name":"Matthew Ruffalo","orcid":"https://orcid.org/0000-0003-2222-6169"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthew Ruffalo","raw_affiliation_strings":["1 Department of Electrical Engineering and Computer Science, 2Department of Genetics and 3Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering and Computer Science, 2Department of Genetics and 3Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043924588","display_name":"Thomas LaFramboise","orcid":"https://orcid.org/0000-0003-1793-4777"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas LaFramboise","raw_affiliation_strings":["1 Department of Electrical Engineering and Computer Science, 2Department of Genetics and 3Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering and Computer Science, 2Department of Genetics and 3Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035558591","display_name":"Mehmet Koyut\u00fcrk","orcid":"https://orcid.org/0000-0002-3434-5512"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mehmet Koyut\u00fcrk","raw_affiliation_strings":["1 Department of Electrical Engineering and Computer Science, 2Department of Genetics and 3Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering and Computer Science, 2Department of Genetics and 3Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5091838807"],"corresponding_institution_ids":["https://openalex.org/I58956616"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":11.7399,"has_fulltext":false,"cited_by_count":235,"citation_normalized_percentile":{"value":0.9916878,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"27","issue":"20","first_page":"2790","last_page":"2796"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9962999820709229,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.7033636569976807},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5364341139793396}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7033636569976807},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5364341139793396}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr477","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr477","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/20/2790/48872412/bioinformatics_27_20_2790.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:21856737","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21856737","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:CiteSeerX.psu:10.1.1.716.2751","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.716.2751","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://compbio.case.edu/koyuturk/publications/ruffalo_bioinformatics_2011.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/20/2790","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/20/2790","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/btr477","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr477","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/20/2790/48872412/bioinformatics_27_20_2790.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":[{"id":"https://metadata.un.org/sdg/12","score":0.5600000023841858,"display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2153805608.pdf","grobid_xml":"https://content.openalex.org/works/W2153805608.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1972924519","https://openalex.org/W1972944037","https://openalex.org/W2000586119","https://openalex.org/W2005129098","https://openalex.org/W2025323279","https://openalex.org/W2045040686","https://openalex.org/W2046601740","https://openalex.org/W2058759221","https://openalex.org/W2075026875","https://openalex.org/W2087064593","https://openalex.org/W2093931624","https://openalex.org/W2097117811","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2106831595","https://openalex.org/W2108075537","https://openalex.org/W2112113834","https://openalex.org/W2115610250","https://openalex.org/W2119923823","https://openalex.org/W2121016876","https://openalex.org/W2124985265","https://openalex.org/W2125826054","https://openalex.org/W2127640118","https://openalex.org/W2139747296","https://openalex.org/W2139760555","https://openalex.org/W2153527981","https://openalex.org/W2155919888","https://openalex.org/W2158322625","https://openalex.org/W2161488606","https://openalex.org/W2162142051","https://openalex.org/W2168909179","https://openalex.org/W2175671778","https://openalex.org/W2799140574","https://openalex.org/W2913199219","https://openalex.org/W2918025614","https://openalex.org/W4247053599","https://openalex.org/W6679808184","https://openalex.org/W6683030939"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","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"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":30},{"year":2015,"cited_by_count":32},{"year":2014,"cited_by_count":37},{"year":2013,"cited_by_count":21},{"year":2012,"cited_by_count":27}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}