{"id":"https://openalex.org/W4213328665","doi":"https://doi.org/10.1371/journal.pcbi.1009269","title":"Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data","display_name":"Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data","publication_year":2022,"publication_date":"2022-02-17","ids":{"openalex":"https://openalex.org/W4213328665","doi":"https://doi.org/10.1371/journal.pcbi.1009269","pmid":"https://pubmed.ncbi.nlm.nih.gov/35176018"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009269","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009269","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009269&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009269&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100387113","display_name":"Ning Wang","orcid":"https://orcid.org/0000-0002-1275-4710"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ning Wang","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0002-1275-4710","affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052696765","display_name":"Vladislav Lysenkov","orcid":"https://orcid.org/0000-0002-1468-1631"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Vladislav Lysenkov","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0002-1468-1631","affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033552410","display_name":"Katri Orte","orcid":"https://orcid.org/0000-0002-0353-6826"},"institutions":[{"id":"https://openalex.org/I2801970007","display_name":"Turku University Hospital","ror":"https://ror.org/05dbzj528","country_code":"FI","type":"healthcare","lineage":["https://openalex.org/I2801970007","https://openalex.org/I4210127022"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Katri Orte","raw_affiliation_strings":["Department of Genomics, Laboratory Division, Turku University Hospital, Turku, Finland","Department of Pathology, Laboratory Division, Turku University Hospital, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0002-0353-6826","affiliations":[{"raw_affiliation_string":"Department of Genomics, Laboratory Division, Turku University Hospital, Turku, Finland","institution_ids":["https://openalex.org/I2801970007"]},{"raw_affiliation_string":"Department of Pathology, Laboratory Division, Turku University Hospital, Turku, Finland","institution_ids":["https://openalex.org/I2801970007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090910971","display_name":"Veli Kairisto","orcid":"https://orcid.org/0000-0002-0562-8054"},"institutions":[{"id":"https://openalex.org/I2801970007","display_name":"Turku University Hospital","ror":"https://ror.org/05dbzj528","country_code":"FI","type":"healthcare","lineage":["https://openalex.org/I2801970007","https://openalex.org/I4210127022"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Veli Kairisto","raw_affiliation_strings":["Department of Genomics, Laboratory Division, Turku University Hospital, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0002-0562-8054","affiliations":[{"raw_affiliation_string":"Department of Genomics, Laboratory Division, Turku University Hospital, Turku, Finland","institution_ids":["https://openalex.org/I2801970007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006055601","display_name":"Juhani Aakko","orcid":"https://orcid.org/0000-0003-4142-3256"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Juhani Aakko","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0003-4142-3256","affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052915247","display_name":"Sofia Khan","orcid":"https://orcid.org/0000-0003-4185-8882"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Sofia Khan","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062339398","display_name":"Laura L. Elo","orcid":"https://orcid.org/0000-0001-5648-4532"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Laura L. Elo","raw_affiliation_strings":["Institute of Biomedicine, University of Turku, Finland","Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0001-5648-4532","affiliations":[{"raw_affiliation_string":"Institute of Biomedicine, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5052915247","https://openalex.org/A5062339398"],"corresponding_institution_ids":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.1699,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.88039321,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"18","issue":"2","first_page":"e1009269","last_page":"e1009269"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9969000220298767,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9966999888420105,"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":0.9717404842376709},{"id":"https://openalex.org/keywords/indel-mutation","display_name":"INDEL Mutation","score":0.6659063696861267},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5972335338592529},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5936828851699829},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.551367998123169},{"id":"https://openalex.org/keywords/1000-genomes-project","display_name":"1000 Genomes Project","score":0.5180602073669434},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46612003445625305},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.4524752199649811},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43282294273376465},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.42434000968933105},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3934357762336731},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2010979950428009},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.18623492121696472}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.9717404842376709},{"id":"https://openalex.org/C2910714999","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"INDEL Mutation","level":5,"score":0.6659063696861267},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5972335338592529},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5936828851699829},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.551367998123169},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.5180602073669434},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46612003445625305},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.4524752199649811},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43282294273376465},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.42434000968933105},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3934357762336731},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2010979950428009},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.18623492121696472},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","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":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1009269","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009269","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009269&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:35176018","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35176018","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:a437cab2e4244fe1ade8f6b8eae33a05","is_oa":true,"landing_page_url":"https://doaj.org/article/a437cab2e4244fe1ade8f6b8eae33a05","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 2, p e1009269 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8916674","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8916674","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:www.utupub.fi:10024/157249","is_oa":false,"landing_page_url":"https://www.utupub.fi/handle/10024/157249","pdf_url":null,"source":{"id":"https://openalex.org/S4306402470","display_name":"UTUPub (University of Turku)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I155660961","host_organization_name":"University of Turku","host_organization_lineage":["https://openalex.org/I155660961"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:www.utupub.fi:10024/188897","is_oa":true,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009269","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009269","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009269","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009269&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1956569869","display_name":null,"funder_award_id":"677943","funder_id":"https://openalex.org/F4320334678","funder_display_name":"European Research Council"},{"id":"https://openalex.org/G263359668","display_name":null,"funder_award_id":"335611","funder_id":"https://openalex.org/F4320323313","funder_display_name":"Turun Yliopisto"},{"id":"https://openalex.org/G4039138905","display_name":null,"funder_award_id":"310561","funder_id":"https://openalex.org/F4320323313","funder_display_name":"Turun Yliopisto"},{"id":"https://openalex.org/G6615885136","display_name":null,"funder_award_id":"296801, 310561, 314443, 329278, 335434, 335611","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320323313","display_name":"Turun Yliopisto","ror":"https://ror.org/05vghhr25"},{"id":"https://openalex.org/F4320323760","display_name":"Sigrid Jus\u00e9liuksen S\u00e4\u00e4ti\u00f6","ror":"https://ror.org/00ckakm23"},{"id":"https://openalex.org/F4320327286","display_name":"Turun Yliopistollinen Keskussairaala","ror":"https://ror.org/05dbzj528"},{"id":"https://openalex.org/F4320328139","display_name":"Biocenter Finland","ror":"https://ror.org/03aay6c48"},{"id":"https://openalex.org/F4320331826","display_name":"Turun Yliopistos\u00e4\u00e4ti\u00f6","ror":null},{"id":"https://openalex.org/F4320334678","display_name":"European Research Council","ror":"https://ror.org/0472cxd90"},{"id":"https://openalex.org/F4320336789","display_name":"Turun yliopiston tutkijakoulu","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4213328665.pdf","grobid_xml":"https://content.openalex.org/works/W4213328665.grobid-xml"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W1964477845","https://openalex.org/W1966936568","https://openalex.org/W1968709543","https://openalex.org/W1980291961","https://openalex.org/W2002438422","https://openalex.org/W2060965924","https://openalex.org/W2075331845","https://openalex.org/W2085755265","https://openalex.org/W2095176401","https://openalex.org/W2095680943","https://openalex.org/W2096823720","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2108472899","https://openalex.org/W2116126626","https://openalex.org/W2119284644","https://openalex.org/W2121679244","https://openalex.org/W2122732537","https://openalex.org/W2138270253","https://openalex.org/W2140869203","https://openalex.org/W2142642738","https://openalex.org/W2146005104","https://openalex.org/W2147733682","https://openalex.org/W2149992227","https://openalex.org/W2154397429","https://openalex.org/W2155306111","https://openalex.org/W2157539385","https://openalex.org/W2157694607","https://openalex.org/W2160344363","https://openalex.org/W2160515792","https://openalex.org/W2161815151","https://openalex.org/W2163938152","https://openalex.org/W2167719367","https://openalex.org/W2168196587","https://openalex.org/W2204914826","https://openalex.org/W2263137078","https://openalex.org/W2297084330","https://openalex.org/W2558202273","https://openalex.org/W2590415818","https://openalex.org/W2742530709","https://openalex.org/W2750673524","https://openalex.org/W2769371660","https://openalex.org/W2770095154","https://openalex.org/W2779975541","https://openalex.org/W2780974917","https://openalex.org/W2787696532","https://openalex.org/W2791189474","https://openalex.org/W2793903215","https://openalex.org/W2867868648","https://openalex.org/W2889664156","https://openalex.org/W2899175097","https://openalex.org/W2948024819","https://openalex.org/W2950919185","https://openalex.org/W2951331911","https://openalex.org/W2951501862","https://openalex.org/W2951529834","https://openalex.org/W2952870794","https://openalex.org/W2953270703","https://openalex.org/W2963186762","https://openalex.org/W2986448893","https://openalex.org/W2990344913","https://openalex.org/W3044880600","https://openalex.org/W3101579057","https://openalex.org/W3134249481","https://openalex.org/W3199243760","https://openalex.org/W4233035577","https://openalex.org/W4394666350","https://openalex.org/W6645148134","https://openalex.org/W6672163627","https://openalex.org/W6683495024","https://openalex.org/W6769616836","https://openalex.org/W6770662217"],"related_works":["https://openalex.org/W1882576502","https://openalex.org/W2529614973","https://openalex.org/W2167094946","https://openalex.org/W3103976079","https://openalex.org/W2160515792","https://openalex.org/W2744064477","https://openalex.org/W4389228387","https://openalex.org/W2043864615","https://openalex.org/W4213020450","https://openalex.org/W2156272823"],"abstract_inverted_index":{"Insertions":[0],"and":[1,38,102,125],"deletions":[2],"(indels)":[3],"in":[4],"human":[5],"genomes":[6],"are":[7],"associated":[8],"with":[9,70,129],"a":[10,56,71,121],"wide":[11,72],"range":[12],"of":[13,28,59,62,74,94,104],"phenotypes,":[14],"including":[15],"various":[16],"clinical":[17],"disorders.":[18],"High-throughput,":[19],"next":[20],"generation":[21],"sequencing":[22],"(NGS)":[23],"technologies":[24,118],"enable":[25],"the":[26,41,60,92,100],"detection":[27],"short":[29],"genetic":[30],"variants,":[31],"such":[32],"as":[33],"single":[34,81],"nucleotide":[35],"variants":[36],"(SNVs)":[37],"indels.":[39],"However,":[40],"variant":[42,63,95,131],"calling":[43,64,96,132],"accuracy":[44],"for":[45,51,66],"indels":[46],"remains":[47],"considerably":[48],"lower":[49],"than":[50],"SNVs.":[52],"Here":[53],"we":[54],"present":[55],"comparative":[57],"study":[58],"performance":[61],"tools":[65],"indel":[67,105],"calling,":[68],"evaluated":[69],"repertoire":[73],"NGS":[75,117],"datasets.":[76],"While":[77],"there":[78],"is":[79,113],"no":[80],"optimal":[82],"tool":[83,97],"to":[84,108,115],"suit":[85],"all":[86],"circumstances,":[87],"our":[88],"results":[89],"demonstrate":[90],"that":[91,119],"choice":[93],"greatly":[98],"impacts":[99],"precision":[101],"recall":[103],"calling.":[106],"Furthermore,":[107],"reliably":[109],"detect":[110],"indels,":[111],"it":[112],"essential":[114],"choose":[116],"offer":[120],"long":[122],"read":[123],"length":[124],"high":[126],"coverage":[127],"coupled":[128],"specific":[130],"tools.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":6}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
