{"id":"https://openalex.org/W4412622732","doi":"https://doi.org/10.21105/joss.08065","title":"seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies","display_name":"seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies","publication_year":2025,"publication_date":"2025-07-24","ids":{"openalex":"https://openalex.org/W4412622732","doi":"https://doi.org/10.21105/joss.08065"},"language":"en","primary_location":{"id":"doi:10.21105/joss.08065","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.08065","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.08065.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.08065.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119061575","display_name":"Ira Zibbu","orcid":null},"institutions":[{"id":"https://openalex.org/I50557253","display_name":"Indian Institute of Science Education and Research Thiruvananthapuram","ror":"https://ror.org/01pe3t004","country_code":"IN","type":"education","lineage":["https://openalex.org/I50557253"]},{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Ira Zibbu","raw_affiliation_strings":["Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America","School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India"],"raw_orcid":"https://orcid.org/0009-0003-3930-5397","affiliations":[{"raw_affiliation_string":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India","institution_ids":["https://openalex.org/I50557253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070411498","display_name":"Claus O. Wilke","orcid":"https://orcid.org/0000-0002-7470-9261"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Claus O. Wilke","raw_affiliation_strings":["Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7470-9261","affiliations":[{"raw_affiliation_string":"Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079232304","display_name":"Jeffrey E. Barrick","orcid":"https://orcid.org/0000-0003-0888-7358"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey E. Barrick","raw_affiliation_strings":["Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-0888-7358","affiliations":[{"raw_affiliation_string":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10551179,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"10","issue":"111","first_page":"8065","last_page":"8065"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.982200026512146,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9746999740600586,"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/structural-variation","display_name":"Structural variation","score":0.8057553768157959},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.6557875871658325},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5802521705627441},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5053077340126038},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4666307866573334},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3942629098892212},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38393765687942505},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15144240856170654},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09621056914329529},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09201681613922119},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07397022843360901}],"concepts":[{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.8057553768157959},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.6557875871658325},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5802521705627441},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5053077340126038},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4666307866573334},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3942629098892212},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38393765687942505},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15144240856170654},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09621056914329529},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09201681613922119},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07397022843360901},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21105/joss.08065","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.08065","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.08065.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.21105/joss.08065","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.08065","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.08065.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6700000166893005,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[{"id":"https://openalex.org/G171288798","display_name":"LTREB Renewal: The Long-Term Evolution Experiment with Escherichia coli","funder_award_id":"1951307","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310620","display_name":"University of Texas at Austin","ror":"https://ror.org/00hj54h04"},{"id":"https://openalex.org/F4320320719","display_name":"Department of Science and Technology, Ministry of Science and Technology, India","ror":"https://ror.org/0101xrq71"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412622732.pdf","grobid_xml":"https://content.openalex.org/works/W4412622732.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W2041257508","https://openalex.org/W2096093282","https://openalex.org/W2105559365","https://openalex.org/W2110417468","https://openalex.org/W2114850508","https://openalex.org/W2156273926","https://openalex.org/W2159656968","https://openalex.org/W2290768068","https://openalex.org/W2726257503","https://openalex.org/W2765745983","https://openalex.org/W2784788330","https://openalex.org/W2788228074","https://openalex.org/W2950354111","https://openalex.org/W2994888090","https://openalex.org/W3164465449","https://openalex.org/W3199385470","https://openalex.org/W4225696641","https://openalex.org/W4382537978","https://openalex.org/W6931422085"],"related_works":["https://openalex.org/W2386430105","https://openalex.org/W2356521405","https://openalex.org/W2038534795","https://openalex.org/W2384358604","https://openalex.org/W1567829292","https://openalex.org/W2043074282","https://openalex.org/W2203319208","https://openalex.org/W3175810792","https://openalex.org/W3140471545","https://openalex.org/W3193218983"],"abstract_inverted_index":{"Zibbu":[0],"et":[1],"al.,":[2],"(2025).":[3],"<em>seabreeze</em>:":[4],"A":[5],"Pipeline":[6],"for":[7],"Analyzing":[8],"Structural":[9],"Variation":[10],"Between":[11],"Bacterial":[12],"Genome":[13],"Assemblies.":[14],"Journal":[15],"of":[16],"Open":[17],"Source":[18],"Software,":[19],"10(111),":[20],"8065,":[21],"https://doi.org/10.21105/joss.08065":[22]},"counts_by_year":[],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
