{"id":"https://openalex.org/W3193453955","doi":"https://doi.org/10.1093/bioinformatics/btab601","title":"indelPost: harmonizing ambiguities in simple and complex indel alignments","display_name":"indelPost: harmonizing ambiguities in simple and complex indel alignments","publication_year":2021,"publication_date":"2021-08-25","ids":{"openalex":"https://openalex.org/W3193453955","doi":"https://doi.org/10.1093/bioinformatics/btab601","mag":"3193453955","pmid":"https://pubmed.ncbi.nlm.nih.gov/34431982"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab601","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab601","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083037720","display_name":"Kohei Hagiwara","orcid":"https://orcid.org/0000-0001-7787-2008"},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kohei Hagiwara","raw_affiliation_strings":["Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"],"raw_orcid":"https://orcid.org/0000-0001-7787-2008","affiliations":[{"raw_affiliation_string":"Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041737379","display_name":"Michael N. Edmonson","orcid":"https://orcid.org/0000-0003-0339-700X"},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael N Edmonson","raw_affiliation_strings":["Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003575856","display_name":"David A. Wheeler","orcid":"https://orcid.org/0000-0002-9056-6299"},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David A Wheeler","raw_affiliation_strings":["Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100436594","display_name":"Jinghui Zhang","orcid":"https://orcid.org/0000-0003-3350-9682"},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jinghui Zhang","raw_affiliation_strings":["Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA","institution_ids":["https://openalex.org/I1313298211"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100436594"],"corresponding_institution_ids":["https://openalex.org/I1313298211"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.6953,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.84828048,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"2","first_page":"549","last_page":"551"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8536999821662903,"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":0.8536999821662903,"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":0.029899999499320984,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.020400000736117363,"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/indel","display_name":"Indel","score":0.8938063383102417},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.7970387935638428},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6540926694869995},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37478935718536377},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3528345823287964},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3225574493408203},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13805612921714783},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11204826831817627}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.8938063383102417},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.7970387935638428},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6540926694869995},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37478935718536377},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3528345823287964},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3225574493408203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13805612921714783},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11204826831817627},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"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":"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":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab601","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab601","pdf_url":null,"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:34431982","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34431982","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W2066852475","https://openalex.org/W2103441770","https://openalex.org/W2107318366","https://openalex.org/W2108996658","https://openalex.org/W2128473676","https://openalex.org/W2138601221","https://openalex.org/W2147733682","https://openalex.org/W2168133698","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2194510225","https://openalex.org/W2867868648","https://openalex.org/W2891815860","https://openalex.org/W2964849163","https://openalex.org/W2980211910","https://openalex.org/W3098304617","https://openalex.org/W3184957690","https://openalex.org/W4226185221"],"related_works":["https://openalex.org/W2033001683","https://openalex.org/W2167094946","https://openalex.org/W4387460329","https://openalex.org/W2046457574","https://openalex.org/W1949458596","https://openalex.org/W4285059642","https://openalex.org/W3144677376","https://openalex.org/W32785519","https://openalex.org/W4382398022","https://openalex.org/W2061730343"],"abstract_inverted_index":{"SUMMARY:":[0],"Small":[1],"insertions":[2],"and":[3,16,38,70,75,88],"deletions":[4],"(indels)":[5],"in":[6,20],"nucleotide":[7],"sequence":[8,23],"may":[9,43],"be":[10],"represented":[11],"differently":[12],"between":[13,35],"mapping":[14],"algorithms":[15],"variant":[17,56,105],"callers,":[18],"or":[19],"the":[21,91,97],"flanking":[22],"context.":[24],"Representational":[25],"ambiguity":[26],"is":[27,122],"especially":[28],"profound":[29],"for":[30,68,114],"complex":[31,71,93,115],"indels,":[32],"complicating":[33],"comparisons":[34],"multiple":[36],"mappings":[37],"call":[39],"sets.":[40],"Complex":[41],"indels":[42,72],"additionally":[44],"suffer":[45],"from":[46,96],"incomplete":[47],"allele":[48],"representation,":[49],"potentially":[50],"leading":[51],"to":[52],"critical":[53],"misannotation":[54],"of":[55,85],"effect.":[57],"We":[58,78],"present":[59],"indelPost,":[60],"a":[61,111],"Python":[62],"library":[63],"that":[64,80],"harmonizes":[65],"these":[66],"ambiguities":[67],"simple":[69,98],"via":[73],"realignment":[74],"read-based":[76],"phasing.":[77],"demonstrate":[79],"indelPost":[81,121],"enables":[82],"accurate":[83],"analysis":[84],"ambiguous":[86],"data":[87,130],"can":[89],"derive":[90],"correct":[92],"indel":[94,99,116],"alleles":[95],"predictions":[100],"provided":[101],"by":[102],"standard":[103],"small":[104],"detectors,":[106],"with":[107],"improved":[108],"performance":[109],"over":[110],"specialized":[112],"tool":[113],"analysis.":[117],"AVAILABILITY":[118],"AND":[119],"IMPLEMENTATION:":[120],"freely":[123],"available":[124,132],"at:":[125],"https://github.com/stjude/indelPost.":[126],"SUPPLEMENTARY":[127],"INFORMATION:":[128],"Supplementary":[129],"are":[131],"at":[133],"Bioinformatics":[134],"online.":[135]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
