{"id":"https://openalex.org/W4415725432","doi":"https://doi.org/10.1093/bioinformatics/btaf599","title":"OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis","display_name":"OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis","publication_year":2025,"publication_date":"2025-10-30","ids":{"openalex":"https://openalex.org/W4415725432","doi":"https://doi.org/10.1093/bioinformatics/btaf599","pmid":"https://pubmed.ncbi.nlm.nih.gov/41169152"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf599","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf599","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btaf599","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000436416","display_name":"Qingxiang Guo","orcid":"https://orcid.org/0000-0002-3694-3428"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qingxiang Guo","raw_affiliation_strings":["Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States"],"affiliations":[{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103203416","display_name":"Yangyang Li","orcid":"https://orcid.org/0000-0001-8224-1067"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yangyang Li","raw_affiliation_strings":["Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States"],"affiliations":[{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082439001","display_name":"Ting-You Wang","orcid":"https://orcid.org/0000-0003-4354-3198"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ting-You Wang","raw_affiliation_strings":["Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States"],"affiliations":[{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083700537","display_name":"Anjali Ramakrishnan","orcid":"https://orcid.org/0000-0002-6557-5206"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abhirami Ramakrishnan","raw_affiliation_strings":["Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States"],"affiliations":[{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"last","author":{"id":null,"display_name":"Rendong Yang","orcid":"https://orcid.org/0000-0002-9512-2240"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]},{"id":"https://openalex.org/I4390039227","display_name":"Robert H. Lurie Comprehensive Cancer Center of Northwestern University","ror":"https://ror.org/02p4far57","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4210147348","https://openalex.org/I4390039227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rendong Yang","raw_affiliation_strings":["Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States"],"affiliations":[{"raw_affiliation_string":"Department of Urology, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","institution_ids":["https://openalex.org/I4390039227"]},{"raw_affiliation_string":"Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States","institution_ids":["https://openalex.org/I111979921"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5000436416"],"corresponding_institution_ids":["https://openalex.org/I111979921"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.21836553,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.10260000079870224,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.10260000079870224,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.08420000225305557,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0746999979019165,"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/software","display_name":"Software","score":0.4805999994277954},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4239000082015991},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4092000126838684},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.2888000011444092},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.26989999413490295}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7121000289916992},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4805999994277954},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4239000082015991},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4092000126838684},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.36250001192092896},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32710000872612},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3239000141620636},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.30709999799728394},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2888000011444092},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2802000045776367},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.26989999413490295},{"id":"https://openalex.org/C2984499602","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Computer software","level":2,"score":0.2619999945163727}],"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":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaf599","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf599","pdf_url":null,"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:41169152","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41169152","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":{"id":"doi:10.1093/bioinformatics/btaf599","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf599","pdf_url":null,"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":[{"id":"https://openalex.org/G4173605594","display_name":null,"funder_award_id":"R01CA259388","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7994378027","display_name":null,"funder_award_id":"R35GM142441","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1912672559","https://openalex.org/W2002438422","https://openalex.org/W2030222772","https://openalex.org/W2107830007","https://openalex.org/W2111350087","https://openalex.org/W2135802610","https://openalex.org/W2146005104","https://openalex.org/W2149992227","https://openalex.org/W2154755614","https://openalex.org/W2235737683","https://openalex.org/W2528483409","https://openalex.org/W2557610530","https://openalex.org/W2789843538","https://openalex.org/W2929354011","https://openalex.org/W2948024819","https://openalex.org/W2949062400","https://openalex.org/W2950121474","https://openalex.org/W2950833487","https://openalex.org/W2951764279","https://openalex.org/W2951882034","https://openalex.org/W2963186762","https://openalex.org/W2980310926","https://openalex.org/W2990344913","https://openalex.org/W3021225320","https://openalex.org/W3034581902","https://openalex.org/W3046401484","https://openalex.org/W3131055609","https://openalex.org/W3147574308","https://openalex.org/W3160770927","https://openalex.org/W3199477560","https://openalex.org/W4210602415","https://openalex.org/W4214821232","https://openalex.org/W4225624933","https://openalex.org/W4226329457","https://openalex.org/W4291950457","https://openalex.org/W4312113735","https://openalex.org/W4313250582","https://openalex.org/W4317034776","https://openalex.org/W4317502116","https://openalex.org/W4390500910","https://openalex.org/W4391232231","https://openalex.org/W4391474878","https://openalex.org/W4392089907","https://openalex.org/W4393072002","https://openalex.org/W4402621858"],"related_works":[],"abstract_inverted_index":{"All":[0],"codes":[1],"are":[2],"available":[3],"at":[4],"https://github.com/ylab-hi/OctopuSV;":[5],"https://github.com/ylab-hi/TentacleSV.":[6]},"counts_by_year":[],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-31T00:00:00"}