{"id":"https://openalex.org/W2091193685","doi":"https://doi.org/10.1186/1471-2105-14-184","title":"Benchmarking short sequence mapping tools","display_name":"Benchmarking short sequence mapping tools","publication_year":2013,"publication_date":"2013-06-07","ids":{"openalex":"https://openalex.org/W2091193685","doi":"https://doi.org/10.1186/1471-2105-14-184","mag":"2091193685","pmid":"https://pubmed.ncbi.nlm.nih.gov/23758764"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-184","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-184","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-184","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/counter/pdf/10.1186/1471-2105-14-184","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054786410","display_name":"Ayat Hatem","orcid":null},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ayat Hatem","raw_affiliation_strings":["Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008376823","display_name":"Doruk Bozda\u011f","orcid":null},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Doruk Bozda\u011f","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048305106","display_name":"Amanda E. Toland","orcid":"https://orcid.org/0000-0002-0271-1792"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amanda E Toland","raw_affiliation_strings":["Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026046737","display_name":"\u00dcmit V. \u00c7ataly\u00fcrek","orcid":"https://orcid.org/0000-0002-5625-3758"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"\u00dcmit V \u00c7ataly\u00fcrek","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA","Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5026046737"],"corresponding_institution_ids":["https://openalex.org/I52357470"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":13.0691,"has_fulltext":true,"cited_by_count":236,"citation_normalized_percentile":{"value":0.99308795,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"14","issue":"1","first_page":"184","last_page":"184"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9815999865531921,"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":0.9815999865531921,"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":0.004800000227987766,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.0015999999595806003,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.9600812196731567},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7409316897392273},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5370762348175049},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5257559418678284},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5151783227920532},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.4283987283706665},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3776693344116211},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.24686706066131592}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.9600812196731567},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7409316897392273},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5370762348175049},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5257559418678284},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5151783227920532},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.4283987283706665},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3776693344116211},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.24686706066131592},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"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":"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":"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":"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":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-14-184","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-184","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-184","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:23758764","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23758764","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:europepmc.org:2688080","is_oa":true,"landing_page_url":"http://europepmc.org/abstract/MED/23758764","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3694458","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3694458","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:10.1186/1471-2105-14-184","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-184","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-184","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":[],"awards":[{"id":"https://openalex.org/G2196207810","display_name":null,"funder_award_id":"CNS-0643969","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4284715938","display_name":null,"funder_award_id":"OCI-0904809","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4794183843","display_name":"Collaborative Research: Taming the scale explosion in nuclear structure calculations","funder_award_id":"0904809","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5285988562","display_name":null,"funder_award_id":"DE-FC02-06ER2775","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7085151851","display_name":null,"funder_award_id":"4-1454-1-233","funder_id":"https://openalex.org/F4320309815","funder_display_name":"Qatar Foundation"},{"id":"https://openalex.org/G7180187929","display_name":"CAREER: Scalable Combinatorial Scientific Computing","funder_award_id":"0643969","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7545585691","display_name":null,"funder_award_id":"OCI-0904802","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8587877427","display_name":"Collaborative Research: Enabling Breakthrough Kinetic Simulations of the Magnetosphere via Multi-zone Petascale Computing","funder_award_id":"0904802","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8684173150","display_name":null,"funder_award_id":"4-1454-1-233","funder_id":"https://openalex.org/F4320332753","funder_display_name":"Qatar National Research Fund"},{"id":"https://openalex.org/G8715765657","display_name":null,"funder_award_id":"R01 CA133461","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320309815","display_name":"Qatar Foundation","ror":"https://ror.org/01cawbq05"},{"id":"https://openalex.org/F4320321038","display_name":"Fonds National de la Recherche Luxembourg","ror":"https://ror.org/039z13y21"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332753","display_name":"Qatar National Research Fund","ror":"https://ror.org/01svaqq28"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2091193685.pdf","grobid_xml":"https://content.openalex.org/works/W2091193685.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1973530293","https://openalex.org/W1974365473","https://openalex.org/W1986262731","https://openalex.org/W1989568035","https://openalex.org/W2000586119","https://openalex.org/W2037113830","https://openalex.org/W2037953066","https://openalex.org/W2044586667","https://openalex.org/W2072193858","https://openalex.org/W2093931624","https://openalex.org/W2096441981","https://openalex.org/W2096760403","https://openalex.org/W2097117811","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2106808791","https://openalex.org/W2112113834","https://openalex.org/W2115610250","https://openalex.org/W2117683095","https://openalex.org/W2119923823","https://openalex.org/W2121016876","https://openalex.org/W2124960286","https://openalex.org/W2124985265","https://openalex.org/W2125826054","https://openalex.org/W2126948011","https://openalex.org/W2131088968","https://openalex.org/W2133687564","https://openalex.org/W2139747296","https://openalex.org/W2143124024","https://openalex.org/W2145186114","https://openalex.org/W2145636602","https://openalex.org/W2152246890","https://openalex.org/W2153527981","https://openalex.org/W2153805608","https://openalex.org/W2156715753","https://openalex.org/W2157539385","https://openalex.org/W2158322625","https://openalex.org/W2161488606","https://openalex.org/W2162277333","https://openalex.org/W2165293958","https://openalex.org/W2168303240","https://openalex.org/W2170551349"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2011676020","https://openalex.org/W2329895846"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,21,173,184,216,234],"development":[2,37],"of":[3,12,14,23,38,58,70,78,181,205,275],"next-generation":[4],"sequencing":[5,107],"instruments":[6],"has":[7],"led":[8],"to":[9,27,75,104,111,222,231,293],"the":[10,36,45,53,56,68,76,79,94,160,163,170,177,200,206,223,260,264,276,280,283,295,299],"generation":[11],"millions":[13],"short":[15],"sequences":[16],"in":[17,194,278,291],"a":[18,28,71,84,101,239,253],"single":[19,189],"run.":[20],"process":[22,236],"aligning":[24],"these":[25],"reads":[26],"reference":[29,171],"genome":[30],"is":[31,83,237,243,269],"time":[32],"consuming":[33],"and":[34,40,55,114,140,146,151,179,226,258],"demands":[35],"fast":[39],"accurate":[41],"alignment":[42],"tools.":[43],"However,":[44,197],"current":[46],"proposed":[47],"tools":[48,108,165,225],"make":[49],"different":[50,261],"compromises":[51],"between":[52],"accuracy":[54],"speed":[57],"mapping.":[59],"Moreover,":[60],"many":[61,246],"important":[62],"aspects":[63,113],"are":[64,153,166,219],"overlooked":[65],"while":[66,208],"comparing":[67],"performance":[69],"newly":[72],"developed":[73],"tool":[74,190,271,296],"state":[77],"art.":[80],"Therefore,":[81,282],"there":[82,268],"need":[85],"for":[86,159,203,212],"an":[87,116],"objective":[88,117],"evaluation":[89],"method":[90],"that":[91,187,242,256,272,297],"covers":[92],"all":[93,192,195,274,279],"aspects.":[95],"In":[96,248],"this":[97,249],"work,":[98,250],"we":[99,251],"introduce":[100],"benchmarking":[102,123,174,217,254],"suite":[103,255],"extensively":[105],"analyze":[106],"with":[109],"respect":[110],"various":[112],"provide":[115],"comparison.":[118],"RESULTS:":[119],"We":[120],"applied":[121,230],"our":[122],"tests":[124,175,207,218],"on":[125,155,168],"9":[126],"well":[127],"known":[128],"mapping":[129,235,265],"tools,":[130],"namely,":[131],"Bowtie,":[132],"Bowtie2,":[133],"BWA,":[134],"SOAP2,":[135],"MAQ,":[136],"RMAP,":[137],"GSNAP,":[138],"Novoalign,":[139],"mrsFAST":[141],"(mrFAST)":[142],"using":[143],"synthetic":[144],"data":[145],"real":[147],"RNA-Seq":[148],"data.":[149],"MAQ":[150],"RMAP":[152],"based":[154,167],"building":[156],"hash":[157],"tables":[158],"reads,":[161],"whereas":[162],"remaining":[164],"indexing":[169],"genome.":[172],"reveal":[176],"strengths":[178],"weaknesses":[180],"each":[182],"tool.":[183],"results":[185],"show":[186],"no":[188,270],"outperforms":[191,273],"others":[193,277],"metrics.":[196],"Bowtie":[198],"maintained":[199],"best":[201,300],"throughput":[202],"most":[204],"BWA":[209],"performed":[210],"better":[211],"longer":[213],"read":[214],"lengths.":[215],"not":[220],"restricted":[221],"mentioned":[224],"can":[227],"be":[228],"further":[229],"others.":[232],"CONCLUSION:":[233],"still":[238],"hard":[240],"problem":[241],"affected":[244],"by":[245],"factors.":[247],"provided":[252],"reveals":[257],"evaluates":[259],"factors":[262],"affecting":[263],"process.":[266],"Still,":[267],"tests.":[281],"end":[284],"user":[285],"should":[286],"clearly":[287],"specify":[288],"his":[289],"needs":[290],"order":[292],"choose":[294],"provides":[298],"results.":[301]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":17},{"year":2018,"cited_by_count":29},{"year":2017,"cited_by_count":24},{"year":2016,"cited_by_count":32},{"year":2015,"cited_by_count":29},{"year":2014,"cited_by_count":31},{"year":2013,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
