{"id":"https://openalex.org/W4391897827","doi":"https://doi.org/10.1093/bioinformatics/btae066","title":"VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs","display_name":"VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs","publication_year":2024,"publication_date":"2024-02-01","ids":{"openalex":"https://openalex.org/W4391897827","doi":"https://doi.org/10.1093/bioinformatics/btae066","pmid":"https://pubmed.ncbi.nlm.nih.gov/38366603"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae066","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae066","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae066/56688449/btae066.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/btae066/56688449/btae066.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103176470","display_name":"Philippe Charron","orcid":"https://orcid.org/0000-0002-9404-2302"},"institutions":[{"id":"https://openalex.org/I1307613440","display_name":"Canadian Food Inspection Agency","ror":"https://ror.org/00qxr8t08","country_code":"CA","type":"funder","lineage":["https://openalex.org/I1307613440"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Philippe Charron","raw_affiliation_strings":["Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road , Nepean, Ontario K2J 4S1, Canada"],"affiliations":[{"raw_affiliation_string":"Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road , Nepean, Ontario K2J 4S1, Canada","institution_ids":["https://openalex.org/I1307613440"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004675827","display_name":"Mingsong Kang","orcid":"https://orcid.org/0000-0002-8795-2973"},"institutions":[{"id":"https://openalex.org/I1307613440","display_name":"Canadian Food Inspection Agency","ror":"https://ror.org/00qxr8t08","country_code":"CA","type":"funder","lineage":["https://openalex.org/I1307613440"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Mingsong Kang","raw_affiliation_strings":["Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road , Nepean, Ontario K2J 4S1, Canada"],"affiliations":[{"raw_affiliation_string":"Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road , Nepean, Ontario K2J 4S1, Canada","institution_ids":["https://openalex.org/I1307613440"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5103176470"],"corresponding_institution_ids":["https://openalex.org/I1307613440"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.6921,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.89946299,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"40","issue":"2","first_page":null,"last_page":null},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9839000105857849,"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/T10066","display_name":"Gut microbiota and health","score":0.9790999889373779,"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/mit-license","display_name":"MIT License","score":0.6429403424263},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.6388253569602966},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5907358527183533},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5873486995697021},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5795626044273376},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5268455743789673},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.5264913439750671},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4761759638786316},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.464804083108902},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3810535669326782},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3337695002555847},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.20318639278411865},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16674759984016418},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.11457395553588867},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07904747128486633}],"concepts":[{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6429403424263},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.6388253569602966},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5907358527183533},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5873486995697021},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5795626044273376},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5268455743789673},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.5264913439750671},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4761759638786316},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.464804083108902},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3810535669326782},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3337695002555847},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.20318639278411865},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16674759984016418},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.11457395553588867},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07904747128486633},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae066","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae066","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae066/56688449/btae066.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:38366603","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38366603","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:10898327","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10898327","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10898327/pdf/btae066.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btae066","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae066","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae066/56688449/btae066.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":[{"id":"https://openalex.org/F4320311580","display_name":"Canadian Food Inspection Agency","ror":"https://ror.org/00qxr8t08"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4391897827.pdf"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W2008338708","https://openalex.org/W2104549677","https://openalex.org/W2106676963","https://openalex.org/W2119180969","https://openalex.org/W2119582595","https://openalex.org/W2144515973","https://openalex.org/W2582800429","https://openalex.org/W2792225186","https://openalex.org/W2795930404","https://openalex.org/W2951149781","https://openalex.org/W2951764279","https://openalex.org/W2952067146","https://openalex.org/W3005014603","https://openalex.org/W3011696475","https://openalex.org/W3046401484","https://openalex.org/W3093528466","https://openalex.org/W3101579057","https://openalex.org/W3175160490","https://openalex.org/W4225764874","https://openalex.org/W4293146479","https://openalex.org/W4307777744","https://openalex.org/W4313430580","https://openalex.org/W4365513261"],"related_works":["https://openalex.org/W4309247532","https://openalex.org/W2604408404","https://openalex.org/W3096946169","https://openalex.org/W2113128227","https://openalex.org/W2144610372","https://openalex.org/W4312114021","https://openalex.org/W4311938462","https://openalex.org/W2121840477","https://openalex.org/W2515936044","https://openalex.org/W3123068371"],"abstract_inverted_index":{"The":[0],"source":[1],"code,":[2],"test":[3],"data,":[4],"and":[5],"relevant":[6],"information":[7],"for":[8],"VD":[9],"are":[10],"freely":[11],"accessible":[12],"at":[13],"https://github.com/OLF-Bioinformatics/VariantDetective":[14],"under":[15],"the":[16],"MIT":[17],"License.":[18]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}