{"id":"https://openalex.org/W1979341154","doi":"https://doi.org/10.1142/s021972001000463x","title":"STATISTICAL COMPARISON OF METHODS TO ESTIMATE THE ERROR PROBABILITY IN SHORT-READ ILLUMINA SEQUENCING","display_name":"STATISTICAL COMPARISON OF METHODS TO ESTIMATE THE ERROR PROBABILITY IN SHORT-READ ILLUMINA SEQUENCING","publication_year":2010,"publication_date":"2010-03-05","ids":{"openalex":"https://openalex.org/W1979341154","doi":"https://doi.org/10.1142/s021972001000463x","mag":"1979341154","pmid":"https://pubmed.ncbi.nlm.nih.gov/20556863"},"language":"en","primary_location":{"id":"doi:10.1142/s021972001000463x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001000463x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032702053","display_name":"Irina Abnizova","orcid":"https://orcid.org/0000-0002-8460-8210"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"IRINA ABNIZOVA","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK","Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054374928","display_name":"Tom Skelly","orcid":null},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"TOM SKELLY","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK","Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017711162","display_name":"Fedor Naumenko","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"FEDOR NAUMENKO","raw_affiliation_strings":["Cratherne Way, Cambridge, CB4 2LZ, UK"],"affiliations":[{"raw_affiliation_string":"Cratherne Way, Cambridge, CB4 2LZ, UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007699018","display_name":"Nava Whiteford","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155982","display_name":"Oxford Nanopore Technologies (United Kingdom)","ror":"https://ror.org/04hyfx005","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210155982"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"NAVA WHITEFORD","raw_affiliation_strings":["Oxford Nanopore, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford. UK. OX4 4GA, UK"],"affiliations":[{"raw_affiliation_string":"Oxford Nanopore, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford. UK. OX4 4GA, UK","institution_ids":["https://openalex.org/I4210155982"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066869533","display_name":"Clive Brown","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155982","display_name":"Oxford Nanopore Technologies (United Kingdom)","ror":"https://ror.org/04hyfx005","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210155982"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"CLIVE BROWN","raw_affiliation_strings":["Oxford Nanopore, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford. UK. OX4 4GA, UK"],"affiliations":[{"raw_affiliation_string":"Oxford Nanopore, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford. UK. OX4 4GA, UK","institution_ids":["https://openalex.org/I4210155982"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112785429","display_name":"Tony Cox","orcid":null},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"TONY COX","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK","Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA UK","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5032702053"],"corresponding_institution_ids":["https://openalex.org/I2802476451"],"apc_list":null,"apc_paid":null,"fwci":0.86652352,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.69395276,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"08","issue":"03","first_page":"579","last_page":"591"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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":0.9983999729156494,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9945999979972839,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9925000071525574,"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/computer-science","display_name":"Computer science","score":0.5849728584289551},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.5665979981422424},{"id":"https://openalex.org/keywords/reliability","display_name":"Reliability (semiconductor)","score":0.49103856086730957},{"id":"https://openalex.org/keywords/calibration","display_name":"Calibration","score":0.4677004814147949},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4146273136138916},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3858136534690857},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2893775999546051},{"id":"https://openalex.org/keywords/power","display_name":"Power (physics)","score":0.19877755641937256},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18900001049041748}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5849728584289551},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.5665979981422424},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.49103856086730957},{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.4677004814147949},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4146273136138916},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3858136534690857},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2893775999546051},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.19877755641937256},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18900001049041748},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"D012984","descriptor_name":"Software","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":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"D012984","descriptor_name":"Software","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":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s021972001000463x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001000463x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:20556863","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20556863","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.699999988079071}],"awards":[],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320312414","display_name":"Oxford Nanopore Technologies","ror":"https://ror.org/04hyfx005"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1532331378","https://openalex.org/W1986473212","https://openalex.org/W2039716761","https://openalex.org/W2059670608","https://openalex.org/W2085060961","https://openalex.org/W2106480442","https://openalex.org/W2119923823","https://openalex.org/W2151732271","https://openalex.org/W4293088719"],"related_works":["https://openalex.org/W4389116644","https://openalex.org/W2153315159","https://openalex.org/W3103844505","https://openalex.org/W259157601","https://openalex.org/W4205463238","https://openalex.org/W1482209366","https://openalex.org/W2110523656","https://openalex.org/W2521627374","https://openalex.org/W2981954115","https://openalex.org/W2901057123"],"abstract_inverted_index":{"As":[0],"was":[1],"the":[2,5,8,11,34,37,39,47,64,81,85,100,120,131,136,157,160,165],"case":[3],"in":[4,46],"beginning":[6],"of":[7,14,22,29,36,49,66,87,99,107,130,140,159],"sequencing":[9,16],"era,":[10],"new":[12],"generation":[13],"short-read":[15],"technologies":[17],"still":[18],"requires":[19],"both":[20],"accuracy":[21],"data":[23,123],"processing":[24],"methods":[25],"and":[26,69,111,134],"reliable":[27],"measures":[28],"that":[30],"accuracy.":[31],"Inspired":[32],"by":[33,83,167],"classic":[35],"genre,":[38],"Phred":[40],"method,":[41],"we":[42],"generalized":[43],"those":[44],"findings":[45],"area":[48],"base":[50],"quality":[51],"value":[52],"calibration.":[53],"We":[54,79,118],"introduce":[55],"a":[56,67,146],"simple,":[57],"straightforward":[58],"statistically":[59],"established":[60],"way":[61,74],"to":[62,70,75,143],"measure":[63],"performance":[65,86],"calibrator,":[68],"find":[71],"an":[72],"optimal":[73],"assess":[76],"its":[77],"reliability.":[78],"illustrate":[80],"method":[82,121],"assessing":[84],"several":[88,115],"calibrators/predictors":[89],"for":[90,114,128,156],"Illumina,":[91],"Genome":[92],"Analyser":[93],"2":[94],"(GA2)":[95],"data.":[96],"The":[97,153],"choice":[98],"best":[101,137],"predictor":[102,138],"is":[103,162],"based":[104],"on":[105,122],"optimization":[106],"validity,":[108],"discriminative":[109],"ability":[110],"discrimination":[112],"power":[113],"candidate":[116],"predictors.":[117],"applied":[119],"from":[124,149,164],"one":[125],"experimental":[126],"run":[127],"genome":[129],"phage":[132],"\u03d5X,":[133],"found":[135],"out":[139],"ten":[141],"candidates":[142],"be":[144],"'Purity',":[145],"statistics":[147],"derived":[148],"corrected":[150],"cluster":[151],"intensities.":[152],"source":[154],"code":[155],"comparison":[158],"predictors":[161],"available":[163],"authors":[166],"request.":[168]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
