{"id":"https://openalex.org/W4409284557","doi":"https://doi.org/10.1093/bioinformatics/btaf136","title":"Sawfish: improving long-read structural variant discovery and genotyping with local haplotype modeling","display_name":"Sawfish: improving long-read structural variant discovery and genotyping with local haplotype modeling","publication_year":2025,"publication_date":"2025-03-29","ids":{"openalex":"https://openalex.org/W4409284557","doi":"https://doi.org/10.1093/bioinformatics/btaf136","pmid":"https://pubmed.ncbi.nlm.nih.gov/40203061"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf136","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf136","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf136/62899142/btaf136.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf136/62899142/btaf136.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067341694","display_name":"Christopher T. Saunders","orcid":"https://orcid.org/0000-0002-0726-7600"},"institutions":[{"id":"https://openalex.org/I68554272","display_name":"Pacific Biosciences (United States)","ror":"https://ror.org/00fcszb13","country_code":"US","type":"company","lineage":["https://openalex.org/I68554272"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christopher T Saunders","raw_affiliation_strings":["Computational Biology, PacBio , Menlo Park, CA 94025,","Computational Biology , Menlo Park, 94025 PacBio, CA"],"raw_orcid":"https://orcid.org/0000-0002-0726-7600","affiliations":[{"raw_affiliation_string":"Computational Biology, PacBio , Menlo Park, CA 94025,","institution_ids":[]},{"raw_affiliation_string":"Computational Biology , Menlo Park, 94025 PacBio, CA","institution_ids":["https://openalex.org/I68554272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071742303","display_name":"James Holt","orcid":"https://orcid.org/0000-0001-6411-9236"},"institutions":[{"id":"https://openalex.org/I68554272","display_name":"Pacific Biosciences (United States)","ror":"https://ror.org/00fcszb13","country_code":"US","type":"company","lineage":["https://openalex.org/I68554272"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James M Holt","raw_affiliation_strings":["Computational Biology, PacBio , Menlo Park, CA 94025,","Computational Biology , Menlo Park, 94025 PacBio, CA"],"raw_orcid":"https://orcid.org/0000-0001-6411-9236","affiliations":[{"raw_affiliation_string":"Computational Biology, PacBio , Menlo Park, CA 94025,","institution_ids":[]},{"raw_affiliation_string":"Computational Biology , Menlo Park, 94025 PacBio, CA","institution_ids":["https://openalex.org/I68554272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056210064","display_name":"Daniel N. Baker","orcid":"https://orcid.org/0000-0002-0513-6893"},"institutions":[{"id":"https://openalex.org/I68554272","display_name":"Pacific Biosciences (United States)","ror":"https://ror.org/00fcszb13","country_code":"US","type":"company","lineage":["https://openalex.org/I68554272"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel N Baker","raw_affiliation_strings":["Computational Biology, PacBio , Menlo Park, CA 94025,","Computational Biology , Menlo Park, 94025 PacBio, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology, PacBio , Menlo Park, CA 94025,","institution_ids":[]},{"raw_affiliation_string":"Computational Biology , Menlo Park, 94025 PacBio, CA","institution_ids":["https://openalex.org/I68554272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024105581","display_name":"Juniper A. Lake","orcid":"https://orcid.org/0000-0001-7628-5645"},"institutions":[{"id":"https://openalex.org/I68554272","display_name":"Pacific Biosciences (United States)","ror":"https://ror.org/00fcszb13","country_code":"US","type":"company","lineage":["https://openalex.org/I68554272"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Juniper A Lake","raw_affiliation_strings":["Computational Biology, PacBio , Menlo Park, CA 94025,","Computational Biology , Menlo Park, 94025 PacBio, CA"],"raw_orcid":"https://orcid.org/0000-0001-7628-5645","affiliations":[{"raw_affiliation_string":"Computational Biology, PacBio , Menlo Park, CA 94025,","institution_ids":[]},{"raw_affiliation_string":"Computational Biology , Menlo Park, 94025 PacBio, CA","institution_ids":["https://openalex.org/I68554272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074781066","display_name":"Jonathan R. Belyeu","orcid":"https://orcid.org/0000-0001-5470-8299"},"institutions":[{"id":"https://openalex.org/I68554272","display_name":"Pacific Biosciences (United States)","ror":"https://ror.org/00fcszb13","country_code":"US","type":"company","lineage":["https://openalex.org/I68554272"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan R Belyeu","raw_affiliation_strings":["Computational Biology, PacBio , Menlo Park, CA 94025,","Computational Biology , Menlo Park, 94025 PacBio, CA"],"raw_orcid":"https://orcid.org/0000-0001-5470-8299","affiliations":[{"raw_affiliation_string":"Computational Biology, PacBio , Menlo Park, CA 94025,","institution_ids":[]},{"raw_affiliation_string":"Computational Biology , Menlo Park, 94025 PacBio, CA","institution_ids":["https://openalex.org/I68554272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070991284","display_name":"Zev Kronenberg","orcid":"https://orcid.org/0000-0002-7627-9808"},"institutions":[{"id":"https://openalex.org/I68554272","display_name":"Pacific Biosciences (United States)","ror":"https://ror.org/00fcszb13","country_code":"US","type":"company","lineage":["https://openalex.org/I68554272"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zev Kronenberg","raw_affiliation_strings":["Computational Biology, PacBio , Menlo Park, CA 94025,","Computational Biology , Menlo Park, 94025 PacBio, CA"],"raw_orcid":"https://orcid.org/0000-0002-7627-9808","affiliations":[{"raw_affiliation_string":"Computational Biology, PacBio , Menlo Park, CA 94025,","institution_ids":[]},{"raw_affiliation_string":"Computational Biology , Menlo Park, 94025 PacBio, CA","institution_ids":["https://openalex.org/I68554272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015326950","display_name":"William J. Rowell","orcid":"https://orcid.org/0000-0002-7422-1194"},"institutions":[{"id":"https://openalex.org/I68554272","display_name":"Pacific Biosciences (United States)","ror":"https://ror.org/00fcszb13","country_code":"US","type":"company","lineage":["https://openalex.org/I68554272"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William J Rowell","raw_affiliation_strings":["Computational Biology, PacBio , Menlo Park, CA 94025,","Computational Biology , Menlo Park, 94025 PacBio, CA"],"raw_orcid":"https://orcid.org/0000-0002-7422-1194","affiliations":[{"raw_affiliation_string":"Computational Biology, PacBio , Menlo Park, CA 94025,","institution_ids":[]},{"raw_affiliation_string":"Computational Biology , Menlo Park, 94025 PacBio, CA","institution_ids":["https://openalex.org/I68554272"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015843320","display_name":"Michael A. Eberle","orcid":"https://orcid.org/0000-0001-8965-1253"},"institutions":[{"id":"https://openalex.org/I68554272","display_name":"Pacific Biosciences (United States)","ror":"https://ror.org/00fcszb13","country_code":"US","type":"company","lineage":["https://openalex.org/I68554272"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael A Eberle","raw_affiliation_strings":["Computational Biology, PacBio , Menlo Park, CA 94025,","Computational Biology , Menlo Park, 94025 PacBio, CA"],"raw_orcid":"https://orcid.org/0000-0001-8965-1253","affiliations":[{"raw_affiliation_string":"Computational Biology, PacBio , Menlo Park, CA 94025,","institution_ids":[]},{"raw_affiliation_string":"Computational Biology , Menlo Park, 94025 PacBio, CA","institution_ids":["https://openalex.org/I68554272"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5067341694"],"corresponding_institution_ids":["https://openalex.org/I68554272"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":30.7068,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.99791474,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"41","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.6676999926567078,"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"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.6676999926567078,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.12129999697208405,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.10949999839067459,"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/haplotype","display_name":"Haplotype","score":0.7519022822380066},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.6381784081459045},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5707260370254517},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4404020309448242},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.413308322429657},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.32471930980682373},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1946413815021515},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.14384448528289795}],"concepts":[{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.7519022822380066},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.6381784081459045},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5707260370254517},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4404020309448242},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.413308322429657},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.32471930980682373},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1946413815021515},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.14384448528289795}],"mesh":[{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf136","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf136","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf136/62899142/btaf136.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40203061","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40203061","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12000528","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12000528","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf136","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf136","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf136/62899142/btaf136.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409284557.pdf","grobid_xml":"https://content.openalex.org/works/W4409284557.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1912672559","https://openalex.org/W2949062400","https://openalex.org/W2968499116","https://openalex.org/W3033870872","https://openalex.org/W3034581902","https://openalex.org/W3047598142","https://openalex.org/W3130788486","https://openalex.org/W3145355063","https://openalex.org/W4210887696","https://openalex.org/W4313250582","https://openalex.org/W4391110654","https://openalex.org/W4409729484"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2378369506","https://openalex.org/W3146762847","https://openalex.org/W2398263405","https://openalex.org/W1965396974","https://openalex.org/W2038331681","https://openalex.org/W1998686087","https://openalex.org/W1981169569","https://openalex.org/W2044943383","https://openalex.org/W2152033571"],"abstract_inverted_index":{"MOTIVATION:":[0],"Structural":[1],"variants":[2],"(SVs)":[3],"play":[4],"an":[5,58,196],"important":[6],"role":[7],"in":[8,81,148,158],"evolutionary":[9],"and":[10,52,74,161,232,244],"functional":[11],"genomics":[12],"but":[13],"are":[14,37,42,246],"challenging":[15,151],"to":[16,71,123,135],"characterize.":[17],"High-accuracy,":[18],"long-read":[19,34,101,225],"sequencing":[20],"can":[21],"substantially":[22],"improve":[23,72],"SV":[24,35,50,59,68,85,102,107,180,226],"characterization":[25],"when":[26],"coupled":[27],"with":[28,182],"effective":[29],"calling":[30,206,227],"methods.":[31],"While":[32],"state-of-the-art":[33,100,179,223],"callers":[36,103,129],"highly":[38],"accurate,":[39],"further":[40],"improvements":[41,157],"achievable":[43],"by":[44],"systematically":[45],"modeling":[46,70],"local":[47],"haplotypes":[48],"during":[49],"discovery":[51],"genotyping.":[53],"RESULTS:":[54],"We":[55],"describe":[56],"sawfish,":[57],"caller":[60],"for":[61,195,224],"mapped":[62],"high-quality":[63],"long":[64],"reads":[65],"incorporating":[66],"systematic":[67],"haplotype":[69],"accuracy":[73,98,115,138,147,228],"resolution.":[75],"Assessment":[76],"against":[77],"the":[78,88,96,113,145,149,183,222],"draft":[79],"Genome":[80],"a":[82],"Bottle":[83],"(GIAB)":[84],"benchmark":[86],"from":[87,121,168],"T2T-HG002-Q100":[89],"diploid":[90],"assembly":[91],"shows":[92,144],"that":[93,127,218],"sawfish":[94,111,137,170,219],"has":[95,171],"highest":[97,114,146,184],"among":[99],"across":[104,229],"every":[105,117],"tested":[106,118],"size":[108],"group.":[109],"Additionally,":[110],"maintains":[112],"at":[116,131,139],"depth":[119],"level":[120],"10-":[122],"32-fold":[124],"coverage,":[125],"such":[126],"other":[128,178,213],"required":[130],"least":[132],"30-fold":[133],"coverage":[134],"match":[136],"15-fold":[140],"coverage.":[141],"Sawfish":[142,238],"also":[143],"GIAB":[150],"medically":[152,162],"relevant":[153,163],"genes":[154],"benchmark,":[155],"demonstrating":[156],"both":[159,230],"comprehensive":[160],"contexts.When":[164],"joint-genotyping":[165],"seven":[166],"samples":[167],"CEPH-1463,":[169],"over":[172],"9000":[173],"more":[174,209],"pedigree-concordant":[175,210],"calls":[176],"than":[177,212],"callers,":[181],"proportion":[185,199],"of":[186,200],"concordant":[187,201],"SVs":[188,202,211],"(81%).":[189],"Sawfish's":[190],"quality":[191],"model":[192],"enables":[193],"selection":[194],"even":[197],"higher":[198],"(88%),":[203],"while":[204],"still":[205],"nearly":[207],"5000":[208],"callers.":[214],"These":[215],"results":[216],"demonstrate":[217],"improves":[220],"on":[221,248],"individual":[231],"joint-sample":[233],"analyses.":[234],"AVAILABILITY":[235],"AND":[236],"IMPLEMENTATION:":[237],"source":[239],"code,":[240],"pre-compiled":[241],"Linux":[242],"binaries,":[243],"documentation":[245],"released":[247],"GitHub:":[249],"https://github.com/PacificBiosciences/sawfish.":[250]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":16},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
