{"id":"https://openalex.org/W4310696373","doi":"https://doi.org/10.1093/bioinformatics/btac785","title":"TransFlow: a Snakemake workflow for transmission analysis of<i>Mycobacterium tuberculosis</i>whole-genome sequencing data","display_name":"TransFlow: a Snakemake workflow for transmission analysis of<i>Mycobacterium tuberculosis</i>whole-genome sequencing data","publication_year":2022,"publication_date":"2022-12-05","ids":{"openalex":"https://openalex.org/W4310696373","doi":"https://doi.org/10.1093/bioinformatics/btac785","pmid":"https://pubmed.ncbi.nlm.nih.gov/36469333"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac785","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac785","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac785/48520926/btac785.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac785/48520926/btac785.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082552036","display_name":"Junhang Pan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210136416","display_name":"Zhejiang Center for Disease Control and Prevention","ror":"https://ror.org/03f015z81","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210136416"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junhang Pan","raw_affiliation_strings":["The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China","institution_ids":["https://openalex.org/I4210136416"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016772356","display_name":"Xiangchen Li","orcid":"https://orcid.org/0009-0001-0078-1877"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiangchen Li","raw_affiliation_strings":["Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101927782","display_name":"Mingwu Zhang","orcid":"https://orcid.org/0000-0002-6472-7423"},"institutions":[{"id":"https://openalex.org/I4210136416","display_name":"Zhejiang Center for Disease Control and Prevention","ror":"https://ror.org/03f015z81","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210136416"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingwu Zhang","raw_affiliation_strings":["The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China","institution_ids":["https://openalex.org/I4210136416"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109447992","display_name":"Yewei Lu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yewei Lu","raw_affiliation_strings":["Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101104316","display_name":"Yelei Zhu","orcid":"https://orcid.org/0000-0002-0781-7967"},"institutions":[{"id":"https://openalex.org/I4210136416","display_name":"Zhejiang Center for Disease Control and Prevention","ror":"https://ror.org/03f015z81","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210136416"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yelei Zhu","raw_affiliation_strings":["The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China","institution_ids":["https://openalex.org/I4210136416"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025102059","display_name":"Kunyang Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210136416","display_name":"Zhejiang Center for Disease Control and Prevention","ror":"https://ror.org/03f015z81","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210136416"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kunyang Wu","raw_affiliation_strings":["The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China","institution_ids":["https://openalex.org/I4210136416"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100643544","display_name":"Yiwen Wu","orcid":"https://orcid.org/0000-0001-6059-7054"},"institutions":[{"id":"https://openalex.org/I114539943","display_name":"Zhejiang Chinese Medical University","ror":"https://ror.org/04epb4p87","country_code":"CN","type":"education","lineage":["https://openalex.org/I114539943"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiwen Wu","raw_affiliation_strings":["Department of Medical Oncology, Zhejiang Chinese Medical University , Hangzhou, Zhejiang 310053, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Oncology, Zhejiang Chinese Medical University , Hangzhou, Zhejiang 310053, China","institution_ids":["https://openalex.org/I114539943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010410409","display_name":"Weixin Wang","orcid":"https://orcid.org/0000-0002-2765-2629"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Weixin Wang","raw_affiliation_strings":["Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100427325","display_name":"Bin Chen","orcid":"https://orcid.org/0000-0002-2882-9756"},"institutions":[{"id":"https://openalex.org/I4210136416","display_name":"Zhejiang Center for Disease Control and Prevention","ror":"https://ror.org/03f015z81","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210136416"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Chen","raw_affiliation_strings":["The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China","institution_ids":["https://openalex.org/I4210136416"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101649333","display_name":"Zhengwei Liu","orcid":"https://orcid.org/0000-0002-5139-659X"},"institutions":[{"id":"https://openalex.org/I4210136416","display_name":"Zhejiang Center for Disease Control and Prevention","ror":"https://ror.org/03f015z81","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210136416"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhengwei Liu","raw_affiliation_strings":["The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China","institution_ids":["https://openalex.org/I4210136416"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100423391","display_name":"Xiaomeng Wang","orcid":"https://orcid.org/0000-0002-2409-2419"},"institutions":[{"id":"https://openalex.org/I4210136416","display_name":"Zhejiang Center for Disease Control and Prevention","ror":"https://ror.org/03f015z81","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210136416"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaomeng Wang","raw_affiliation_strings":["The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China","institution_ids":["https://openalex.org/I4210136416"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057775352","display_name":"Junshun Gao","orcid":"https://orcid.org/0000-0001-9040-2289"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Junshun Gao","raw_affiliation_strings":["Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China"],"raw_orcid":"https://orcid.org/0000-0001-9040-2289","affiliations":[{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5057775352","https://openalex.org/A5100423391","https://openalex.org/A5101649333"],"corresponding_institution_ids":["https://openalex.org/I4210136416"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7056,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.71000916,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10038","display_name":"Tuberculosis Research and Epidemiology","score":0.9115999937057495,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10038","display_name":"Tuberculosis Research and Epidemiology","score":0.9115999937057495,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11316","display_name":"Mycobacterium research and diagnosis","score":0.015399999916553497,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12578","display_name":"Diagnosis and treatment of tuberculosis","score":0.012199999764561653,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7403412461280823},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6860412359237671},{"id":"https://openalex.org/keywords/transmission","display_name":"Transmission (telecommunications)","score":0.6455212831497192},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5498499870300293},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5075034499168396},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4774233102798462},{"id":"https://openalex.org/keywords/mycobacterium-tuberculosis","display_name":"Mycobacterium tuberculosis","score":0.4615573585033417},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.45821326971054077},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.4283655881881714},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4159466028213501},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41195985674858093},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.35224008560180664},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20404279232025146},{"id":"https://openalex.org/keywords/tuberculosis","display_name":"Tuberculosis","score":0.19035643339157104},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17699086666107178},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14686629176139832},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1266007423400879}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7403412461280823},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6860412359237671},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.6455212831497192},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5498499870300293},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5075034499168396},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4774233102798462},{"id":"https://openalex.org/C2777975735","wikidata":"https://www.wikidata.org/wiki/Q130971","display_name":"Mycobacterium tuberculosis","level":3,"score":0.4615573585033417},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.45821326971054077},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.4283655881881714},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4159466028213501},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41195985674858093},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.35224008560180664},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20404279232025146},{"id":"https://openalex.org/C2781069245","wikidata":"https://www.wikidata.org/wiki/Q12204","display_name":"Tuberculosis","level":2,"score":0.19035643339157104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17699086666107178},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14686629176139832},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1266007423400879},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","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":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D014376","descriptor_name":"Tuberculosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014376","descriptor_name":"Tuberculosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014376","descriptor_name":"Tuberculosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac785","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac785","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac785/48520926/btac785.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:36469333","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36469333","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:9825751","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825751","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/btac785","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac785","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac785/48520926/btac785.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":[{"display_name":"Good health and well-being","score":0.800000011920929,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321160","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71"},{"id":"https://openalex.org/F4320321851","display_name":"Fudan University","ror":"https://ror.org/013q1eq08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4310696373.pdf","grobid_xml":"https://content.openalex.org/works/W4310696373.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1274794040","https://openalex.org/W1981671702","https://openalex.org/W2019790854","https://openalex.org/W2026203290","https://openalex.org/W2056185169","https://openalex.org/W2060919531","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2110417468","https://openalex.org/W2111281047","https://openalex.org/W2131271579","https://openalex.org/W2143679259","https://openalex.org/W2146290595","https://openalex.org/W2159675211","https://openalex.org/W2159954944","https://openalex.org/W2168133698","https://openalex.org/W2168358002","https://openalex.org/W2187433067","https://openalex.org/W2308769335","https://openalex.org/W2394548811","https://openalex.org/W2432815617","https://openalex.org/W2437467664","https://openalex.org/W2520358661","https://openalex.org/W2558519010","https://openalex.org/W2558624268","https://openalex.org/W2577533595","https://openalex.org/W2585492154","https://openalex.org/W2726949079","https://openalex.org/W2765745983","https://openalex.org/W2766648240","https://openalex.org/W2896693913","https://openalex.org/W2897223716","https://openalex.org/W2901029329","https://openalex.org/W2924537978","https://openalex.org/W2949845804","https://openalex.org/W2951384372","https://openalex.org/W2951825561","https://openalex.org/W2951851640","https://openalex.org/W2952463453","https://openalex.org/W2970329550","https://openalex.org/W2972533591","https://openalex.org/W2990312921","https://openalex.org/W2993967000","https://openalex.org/W2995834440","https://openalex.org/W3009705041","https://openalex.org/W3128373761","https://openalex.org/W3158124116","https://openalex.org/W3168924500","https://openalex.org/W4210556001","https://openalex.org/W6718575244","https://openalex.org/W6731902304","https://openalex.org/W6764248685","https://openalex.org/W6794784586"],"related_works":["https://openalex.org/W3181407718","https://openalex.org/W2364921833","https://openalex.org/W2302028273","https://openalex.org/W1525643724","https://openalex.org/W2067938758","https://openalex.org/W2382623646","https://openalex.org/W3087771547","https://openalex.org/W2333420780","https://openalex.org/W2375199418","https://openalex.org/W2936979086"],"abstract_inverted_index":{"MOTIVATION:":[0],"Whole-genome":[1],"sequencing":[2,78],"(WGS)":[3],"is":[4,137],"increasingly":[5],"used":[6],"to":[7,72,117,129],"aid":[8],"the":[9,23],"understanding":[10],"of":[11,19,30],"Mycobacterium":[12],"tuberculosis":[13,20],"(MTB)":[14],"transmission.":[15],"The":[16],"epidemiological":[17],"analysis":[18,36,65,75],"based":[21],"on":[22,113],"WGS":[24],"technique":[25],"requires":[26],"a":[27,39,57,108],"diverse":[28],"collection":[29],"bioinformatics":[31],"tools.":[32],"Effectively":[33],"using":[34],"these":[35],"tools":[37,71],"in":[38,107],"scalable":[40],"and":[41,61,85,95,104,115,124],"reproducible":[42],"way":[43],"can":[44,125],"be":[45,126],"challenging,":[46],"especially":[47],"for":[48],"non-experts.":[49],"RESULTS:":[50],"Here,":[51],"we":[52],"present":[53],"TransFlow":[54,67,111,136],"(Transmission":[55],"Workflow),":[56],"user-friendly,":[58],"fast,":[59],"efficient":[60],"comprehensive":[62],"WGS-based":[63],"transmission":[64,74,90,92,96],"pipeline.":[66],"combines":[68],"some":[69],"state-of-the-art":[70],"take":[73],"from":[76],"raw":[77],"data,":[79],"through":[80],"quality":[81],"control,":[82],"sequence":[83],"alignment":[84],"variant":[86],"calling,":[87],"into":[88],"downstream":[89],"clustering,":[91],"network":[93],"reconstruction":[94],"risk":[97],"factor":[98],"inference,":[99],"together":[100],"with":[101],"summary":[102,109],"statistics":[103],"data":[105,145],"visualization":[106],"report.":[110],"relies":[112],"Snakemake":[114],"Conda":[116],"resolve":[118],"dependencies":[119],"among":[120],"consecutive":[121],"processing":[122],"steps":[123],"easily":[127],"adapted":[128],"any":[130],"computation":[131],"environment.":[132],"AVAILABILITY":[133],"AND":[134],"IMPLEMENTATION:":[135],"free":[138],"available":[139,147],"at":[140,148],"https://github.com/cvn001/transflow.":[141],"SUPPLEMENTARY":[142],"INFORMATION:":[143],"Supplementary":[144],"are":[146],"Bioinformatics":[149],"online.":[150]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2022-12-15T00:00:00"}
