{"id":"https://openalex.org/W2140673900","doi":"https://doi.org/10.1093/nar/gku370","title":"mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications","display_name":"mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications","publication_year":2014,"publication_date":"2014-05-08","ids":{"openalex":"https://openalex.org/W2140673900","doi":"https://doi.org/10.1093/nar/gku370","mag":"2140673900","pmid":"https://pubmed.ncbi.nlm.nih.gov/24810850"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gku370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku370","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W494/7441754/gku370.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/42/W1/W494/7441754/gku370.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006644128","display_name":"Faraz Hach","orcid":"https://orcid.org/0000-0003-1143-0172"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Faraz Hach","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6 fhach@sfu.ca","School of Computing Science, Simon Fraser University, Burnaby, BC, Canada\u2009V5A\u20091S6"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6 fhach@sfu.ca","institution_ids":[]},{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada\u2009V5A\u20091S6","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085865605","display_name":"Iman Sarrafi","orcid":null},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Iman Sarrafi","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6","School of Computing Science, Simon Fraser University, Burnaby, BC, Canada\u2009V5A\u20091S6"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada\u2009V5A\u20091S6","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016230870","display_name":"Farhad Hormozdiari","orcid":"https://orcid.org/0000-0002-5617-6174"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Farhad Hormozdiari","raw_affiliation_strings":["Computer Science Department, University of California, Los Angeles, CA, USA, 90095"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of California, Los Angeles, CA, USA, 90095","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074885623","display_name":"Can Alkan","orcid":"https://orcid.org/0000-0002-5443-0706"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Can Alkan","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, 06800 Ankara, Turkey","Department of Computer Engineering Bilkent University 06800, Ankara, Turkey"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, 06800 Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Department of Computer Engineering Bilkent University 06800, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014870107","display_name":"Evan E. Eichler","orcid":"https://orcid.org/0000-0002-8246-4014"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Evan E. Eichler","raw_affiliation_strings":["Department of Genome Sciences, University of Washington, Seattle, WA, USA, 98195"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington, Seattle, WA, USA, 98195","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102972238","display_name":"S. Cenk \u015eahinalp","orcid":"https://orcid.org/0000-0002-2170-2808"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"S. Cenk Sahinalp","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6 School of Informatics and Computing, Indiana University, Bloomington, IN, USA, 47405 cenk@sfu.ca","5School of Informatics and Computing, Indiana University, Bloomington, IN, USA, 47405","1School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6 School of Informatics and Computing, Indiana University, Bloomington, IN, USA, 47405 cenk@sfu.ca","institution_ids":[]},{"raw_affiliation_string":"5School of Informatics and Computing, Indiana University, Bloomington, IN, USA, 47405","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"1School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5006644128"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.9932,"has_fulltext":true,"cited_by_count":72,"citation_normalized_percentile":{"value":0.9462746,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"42","issue":"W1","first_page":"W494","last_page":"W500"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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":0.9987000226974487,"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/T11482","display_name":"RNA modifications and cancer","score":0.9937000274658203,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9894999861717224,"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/biology","display_name":"Biology","score":0.9454642534255981},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5538184642791748},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.509460985660553},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4893204867839813},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.48731550574302673},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.2513658404350281},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.20183563232421875},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17797362804412842},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.16565930843353271}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9454642534255981},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5538184642791748},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.509460985660553},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4893204867839813},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.48731550574302673},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.2513658404350281},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.20183563232421875},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17797362804412842},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.16565930843353271}],"mesh":[{"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":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":"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":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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1093/nar/gku370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku370","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W494/7441754/gku370.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:24810850","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24810850","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1003.6648","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1003.6648","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://yoksis.bilkent.edu.tr/pdf/files/8296.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1005.9849","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1005.9849","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/early/2014/05/08/nar.gku370.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.772.7792","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.772.7792","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/b8/85/gku370.PMC4086126.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.995.6139","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.995.6139","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/42/W1/W494.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:3176859","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4086126","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/12707","is_oa":true,"landing_page_url":"http://hdl.handle.net/11693/12707","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research","raw_type":"Article"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/25736","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/25736","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/nar/gku370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku370","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W494/7441754/gku370.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4539561046","display_name":null,"funder_award_id":"HG006004","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334576","display_name":"Canadian Cancer Society Research Institute","ror":"https://ror.org/017343w90"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2140673900.pdf","grobid_xml":"https://content.openalex.org/works/W2140673900.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1828154403","https://openalex.org/W2000160799","https://openalex.org/W2000586119","https://openalex.org/W2022986961","https://openalex.org/W2025648894","https://openalex.org/W2049997041","https://openalex.org/W2083870688","https://openalex.org/W2096441981","https://openalex.org/W2096791516","https://openalex.org/W2097341408","https://openalex.org/W2099642610","https://openalex.org/W2103011829","https://openalex.org/W2103441770","https://openalex.org/W2107688500","https://openalex.org/W2112893969","https://openalex.org/W2113312463","https://openalex.org/W2119305840","https://openalex.org/W2124985265","https://openalex.org/W2127634492","https://openalex.org/W2128114769","https://openalex.org/W2129714591","https://openalex.org/W2133687564","https://openalex.org/W2134199796","https://openalex.org/W2138336970","https://openalex.org/W2139747296","https://openalex.org/W2140154634","https://openalex.org/W2143124024","https://openalex.org/W2149992227","https://openalex.org/W2153527981","https://openalex.org/W2153805608","https://openalex.org/W2157057843","https://openalex.org/W2158322625","https://openalex.org/W2159640103","https://openalex.org/W2159921413","https://openalex.org/W2161488606","https://openalex.org/W2165293958","https://openalex.org/W2168303240","https://openalex.org/W2170551349","https://openalex.org/W2171777347","https://openalex.org/W2497101904","https://openalex.org/W2885727518","https://openalex.org/W6638564077","https://openalex.org/W6675176472","https://openalex.org/W6681016323","https://openalex.org/W6682761550","https://openalex.org/W6683030939","https://openalex.org/W6683504902"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191","https://openalex.org/W2117258802"],"abstract_inverted_index":{"High":[0],"throughput":[1],"sequencing":[2],"(HTS)":[3],"platforms":[4],"generate":[5],"unprecedented":[6],"amounts":[7],"of":[8,26,44,81,96,118,127,139,216,229,322,334,336],"data":[9],"that":[10,20,76,106,138,166,202,218,227,270,335],"introduce":[11,68],"challenges":[12],"for":[13,41,61,158,181,263,324],"processing":[14],"and":[15,102,161,239,245,257,259,305,342],"downstream":[16,45],"analysis.":[17],"While":[18],"tools":[19,287],"report":[21,57,297],"the":[22,79,110,116,125,128,154,200,214,223,230,236,313,325],"'best'":[23],"mapping":[24,59,156,171],"location":[25],"each":[27,62,159],"read":[28,93],"provide":[29],"a":[30,70],"fast":[31],"way":[32],"to":[33,56,151,195,222,283],"process":[34],"HTS":[35,82],"data,":[36],"they":[37],"are":[38,233,240,247],"not":[39,108,241],"suitable":[40],"many":[42],"types":[43],"analysis":[46],"such":[47,147,288],"as":[48,148,289],"structural":[49],"variation":[50],"detection,":[51],"where":[52],"it":[53,191,291,343],"is":[54,133,188,272,292,331,339],"important":[55],"multiple":[58,254],"loci":[60,157,172],"read.":[63],"For":[64],"this":[65,211],"purpose":[66],"we":[67],"mrsFAST-Ultra,":[69],"fast,":[71],"cache":[72,91],"oblivious,":[73],"SNP-aware":[74],"aligner":[75,94],"can":[77,192,219,260,296,344],"handle":[78],"multi-mapping":[80,98,314],"reads":[83,165,194,217],"very":[84],"efficiently.":[85,250],"mrsFAST-Ultra":[86,132,143,187,252,271,317,338],"improves":[87],"mrsFAST,":[88],"our":[89],"first":[90],"oblivious":[92],"capable":[95],"handling":[97],"reads,":[99],"through":[100],"new":[101,145],"compact":[103],"index":[104,129,237,320],"structures":[105],"reduce":[107],"only":[109],"overall":[111],"memory":[112,265],"usage":[113],"but":[114],"also":[115],"number":[117,215],"CPU":[119],"operations":[120],"per":[121,303],"alignment.":[122],"In":[123,281],"fact":[124],"size":[126,321],"generated":[130],"by":[131,209],"10":[134,298],"times":[135,275,299,309],"smaller":[136],"than":[137,277],"mrsFAST.":[140,280],"As":[141],"importantly,":[142],"introduces":[144],"features":[146,232],"being":[149],"able":[150],"(i)":[152],"obtain":[153],"best":[155],"read,":[160],"(ii)":[162],"return":[163],"all":[164,228],"have":[167],"at":[168,204,347],"most":[169],"n":[170],"(within":[173],"an":[174,319],"error":[175],"threshold),":[176],"together":[177],"with":[178],"these":[179],"loci,":[180],"any":[182],"user":[183],"specified":[184],"n.":[185],"Furthermore,":[186,316],"SNP-aware,":[189],"i.e.":[190],"map":[193],"reference":[196,224,328],"genome":[197],"while":[198],"discounting":[199],"mismatches":[201],"occur":[203],"common":[205],"SNP":[206],"locations":[207],"provided":[208],"db-SNP;":[210],"significantly":[212],"increases":[213],"be":[220,261,345],"mapped":[221],"genome.":[225],"Notice":[226],"above":[231],"implemented":[234],"within":[235],"structure":[238],"simple":[242],"post-processing":[243],"steps":[244],"thus":[246],"performed":[248],"highly":[249],"Finally,":[251],"utilizes":[253],"available":[255],"cores":[256],"processors":[258],"tuned":[262],"various":[264],"settings.":[266],"Our":[267],"results":[268],"show":[269],"roughly":[273,332],"five":[274],"faster":[276,307],"its":[278],"predecessor":[279],"comparison":[282],"newly":[284],"enhanced":[285],"popular":[286],"Bowtie2,":[290],"more":[293,301],"sensitive":[294],"(it":[295],"or":[300,310],"mappings":[302],"read)":[304],"much":[306],"(six":[308],"more)":[311],"in":[312],"mode.":[315],"has":[318],"2GB":[323],"entire":[326],"human":[327],"genome,":[329],"which":[330],"half":[333],"Bowtie2.":[337],"open":[340],"source":[341],"accessed":[346],"http://mrsfast.sourceforge.net.":[348]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
