{"id":"https://openalex.org/W4384926450","doi":"https://doi.org/10.1186/s12859-023-05414-w","title":"CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter","display_name":"CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter","publication_year":2023,"publication_date":"2023-07-20","ids":{"openalex":"https://openalex.org/W4384926450","doi":"https://doi.org/10.1186/s12859-023-05414-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/37474912"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05414-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05414-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05414-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05414-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047330196","display_name":"Irene Ortega-Sanz","orcid":"https://orcid.org/0000-0002-5211-1699"},"institutions":[{"id":"https://openalex.org/I46176106","display_name":"Universidad de Burgos","ror":"https://ror.org/049da5t36","country_code":"ES","type":"education","lineage":["https://openalex.org/I46176106"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Irene Ortega-Sanz","raw_affiliation_strings":["Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain","institution_ids":["https://openalex.org/I46176106"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039605195","display_name":"Jos\u00e9 A. Barbero\u2010Aparicio","orcid":"https://orcid.org/0000-0002-3269-0806"},"institutions":[{"id":"https://openalex.org/I46176106","display_name":"Universidad de Burgos","ror":"https://ror.org/049da5t36","country_code":"ES","type":"education","lineage":["https://openalex.org/I46176106"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Jos\u00e9 A. Barbero-Aparicio","raw_affiliation_strings":["Department of Computer Science, University of Burgos, 09006, Burgos, Spain. jabarbero@ubu.es","Department of Computer Science, University of Burgos, 09006, Burgos, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Burgos, 09006, Burgos, Spain. jabarbero@ubu.es","institution_ids":["https://openalex.org/I46176106"]},{"raw_affiliation_string":"Department of Computer Science, University of Burgos, 09006, Burgos, Spain","institution_ids":["https://openalex.org/I46176106"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016056338","display_name":"Antonio Canepa","orcid":"https://orcid.org/0000-0002-0608-2743"},"institutions":[{"id":"https://openalex.org/I46176106","display_name":"Universidad de Burgos","ror":"https://ror.org/049da5t36","country_code":"ES","type":"education","lineage":["https://openalex.org/I46176106"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Antonio Canepa-Oneto","raw_affiliation_strings":["Department of Computer Science, University of Burgos, 09006, Burgos, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Burgos, 09006, Burgos, Spain","institution_ids":["https://openalex.org/I46176106"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075363624","display_name":"Jordi Rovira","orcid":"https://orcid.org/0000-0001-6664-9484"},"institutions":[{"id":"https://openalex.org/I46176106","display_name":"Universidad de Burgos","ror":"https://ror.org/049da5t36","country_code":"ES","type":"education","lineage":["https://openalex.org/I46176106"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jordi Rovira","raw_affiliation_strings":["Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain","institution_ids":["https://openalex.org/I46176106"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052647804","display_name":"Beatriz Melero","orcid":"https://orcid.org/0000-0001-8982-8186"},"institutions":[{"id":"https://openalex.org/I46176106","display_name":"Universidad de Burgos","ror":"https://ror.org/049da5t36","country_code":"ES","type":"education","lineage":["https://openalex.org/I46176106"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Beatriz Melero","raw_affiliation_strings":["Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain. bmelero@ubu.es","Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain. bmelero@ubu.es","institution_ids":["https://openalex.org/I46176106"]},{"raw_affiliation_string":"Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain","institution_ids":["https://openalex.org/I46176106"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5039605195","https://openalex.org/A5052647804"],"corresponding_institution_ids":["https://openalex.org/I46176106"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.936,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.84934368,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"24","issue":"1","first_page":"291","last_page":"291"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":0.9747999906539917,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":0.9747999906539917,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.00279999990016222,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.002199999988079071,"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/workflow","display_name":"Workflow","score":0.6469042301177979},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.4928038418292999},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4742269217967987},{"id":"https://openalex.org/keywords/campylobacter","display_name":"Campylobacter","score":0.4705674350261688},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4451926648616791},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4255269169807434},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4141579866409302},{"id":"https://openalex.org/keywords/typing","display_name":"Typing","score":0.4125930368900299},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3643520772457123},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.29011768102645874},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25768789649009705},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.19960066676139832},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1743517816066742},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.10911846160888672}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6469042301177979},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.4928038418292999},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4742269217967987},{"id":"https://openalex.org/C2779910956","wikidata":"https://www.wikidata.org/wiki/Q131488","display_name":"Campylobacter","level":3,"score":0.4705674350261688},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4451926648616791},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4255269169807434},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4141579866409302},{"id":"https://openalex.org/C2781209916","wikidata":"https://www.wikidata.org/wiki/Q3215756","display_name":"Typing","level":2,"score":0.4125930368900299},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3643520772457123},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29011768102645874},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25768789649009705},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.19960066676139832},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1743517816066742},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.10911846160888672}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002167","descriptor_name":"Campylobacter","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002167","descriptor_name":"Campylobacter","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002167","descriptor_name":"Campylobacter","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-023-05414-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05414-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05414-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37474912","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37474912","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:archive.ugent.be:01JE0X303VYPYVPY9QYE6RWJF9","is_oa":true,"landing_page_url":"https://biblio.ugent.be/publication/01JE0X303VYPYVPY9QYE6RWJF9","pdf_url":"https://biblio.ugent.be/publication/01JE0X303VYPYVPY9QYE6RWJF9/file/01JJ1BJ31H57205RXZYHGTEJ5R.pdf","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"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":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10357626","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10357626","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10357626/pdf/12859_2023_Article_5414.pdf","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:2fea7ed9d0194af7bb0a33d684e085e4","is_oa":true,"landing_page_url":"https://doaj.org/article/2fea7ed9d0194af7bb0a33d684e085e4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-14 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05414-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05414-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05414-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G47987599","display_name":null,"funder_award_id":"LCF/PR/PR18/51130007","funder_id":"https://openalex.org/F4320330256","funder_display_name":"Fundaci\u00f3n Bancaria Caixa d'Estalvis i Pensions de Barcelona"},{"id":"https://openalex.org/G8174545966","display_name":null,"funder_award_id":"LCF/PR/PR18/51130007","funder_id":"https://openalex.org/F4320312058","funder_display_name":"\u201cla Caixa\u201d Foundation"}],"funders":[{"id":"https://openalex.org/F4320312058","display_name":"\u201cla Caixa\u201d Foundation","ror":"https://ror.org/03zhx9h04"},{"id":"https://openalex.org/F4320319138","display_name":"Universidad de Burgos","ror":"https://ror.org/049da5t36"},{"id":"https://openalex.org/F4320328351","display_name":"Junta de Castilla y Le\u00f3n","ror":"https://ror.org/02s8dab97"},{"id":"https://openalex.org/F4320330256","display_name":"Fundaci\u00f3n Bancaria Caixa d'Estalvis i Pensions de Barcelona","ror":null},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4384926450.pdf"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W1849301422","https://openalex.org/W1986708244","https://openalex.org/W1994458586","https://openalex.org/W2041257508","https://openalex.org/W2042107321","https://openalex.org/W2096093282","https://openalex.org/W2099837668","https://openalex.org/W2101305463","https://openalex.org/W2107772251","https://openalex.org/W2118688136","https://openalex.org/W2119497560","https://openalex.org/W2120902911","https://openalex.org/W2120904752","https://openalex.org/W2121180999","https://openalex.org/W2122673596","https://openalex.org/W2131271579","https://openalex.org/W2134852597","https://openalex.org/W2143325926","https://openalex.org/W2157107905","https://openalex.org/W2396849069","https://openalex.org/W2406250479","https://openalex.org/W2432815617","https://openalex.org/W2513727910","https://openalex.org/W2551267404","https://openalex.org/W2557776122","https://openalex.org/W2589432356","https://openalex.org/W2748532813","https://openalex.org/W2765268335","https://openalex.org/W2765745983","https://openalex.org/W2766330607","https://openalex.org/W2801006204","https://openalex.org/W2808713854","https://openalex.org/W2883251903","https://openalex.org/W2888885174","https://openalex.org/W2889554561","https://openalex.org/W2891078715","https://openalex.org/W2901550377","https://openalex.org/W2912320302","https://openalex.org/W2917207851","https://openalex.org/W2936373164","https://openalex.org/W2951043046","https://openalex.org/W2965279968","https://openalex.org/W2990427812","https://openalex.org/W2990618091","https://openalex.org/W2991157178","https://openalex.org/W2996188899","https://openalex.org/W3007189093","https://openalex.org/W3009469344","https://openalex.org/W3042596265","https://openalex.org/W3046570683","https://openalex.org/W3046929726","https://openalex.org/W3126533299","https://openalex.org/W3130121249","https://openalex.org/W3137279194","https://openalex.org/W3159501357","https://openalex.org/W3166553882","https://openalex.org/W3170689505","https://openalex.org/W3210058781","https://openalex.org/W3216208327","https://openalex.org/W3216808825","https://openalex.org/W4200000976","https://openalex.org/W4211166583","https://openalex.org/W4221023137","https://openalex.org/W4251057967","https://openalex.org/W4254687493","https://openalex.org/W4287143612","https://openalex.org/W4311237927","https://openalex.org/W4321230695","https://openalex.org/W4382181953"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W1911163028","https://openalex.org/W3089773112","https://openalex.org/W2181751254","https://openalex.org/W2263699433","https://openalex.org/W1989895641","https://openalex.org/W2467039083","https://openalex.org/W2128247100","https://openalex.org/W4387902646","https://openalex.org/W2149356504"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,152],"rapid":[2],"expansion":[3],"of":[4,11,30,64,67,76,86,95,131,156,159,191],"Whole-Genome":[5],"Sequencing":[6],"has":[7],"revolutionized":[8],"the":[9,28,61,73,84,87,189],"fields":[10],"clinical":[12],"and":[13,41,99,112,125,129,138,149,181],"food":[14],"microbiology.":[15],"However,":[16],"its":[17],"implementation":[18],"as":[19,55,173],"a":[20,33,56,80,174],"routine":[21],"laboratory":[22],"technique":[23],"remains":[24],"challenging":[25],"due":[26],"to":[27,97,101,187],"growth":[29],"data":[31,66,147],"at":[32,203],"faster":[34],"rate":[35],"than":[36],"can":[37],"be":[38],"effectively":[39],"analyzed":[40],"critical":[42],"gaps":[43],"in":[44,140,171],"bioinformatics":[45,58,172],"knowledge.":[46],"RESULTS:":[47],"To":[48],"address":[49],"both":[50],"issues,":[51],"CamPype":[52,91,157,199],"was":[53],"developed":[54],"new":[57],"workflow":[59,161],"for":[60,119,145,165,178,195],"genomics":[62],"analysis":[63],"sequencing":[65],"bacteria,":[68],"especially":[69],"Campylobacter,":[70],"which":[71],"is":[72,200],"main":[74],"cause":[75],"gastroenteritis":[77],"worldwide":[78],"making":[79],"negative":[81],"impact":[82],"on":[83],"economy":[85],"public":[88],"health":[89],"systems.":[90],"allows":[92],"fully":[93],"customization":[94],"stages":[96],"run":[98],"tools":[100],"use,":[102],"including":[103],"read":[104,108],"quality":[105],"control":[106],"filtering,":[107],"contamination,":[109],"reads":[110],"extension":[111],"assembly,":[113],"bacterial":[114,179],"typing,":[115],"genome":[116],"annotation,":[117],"searching":[118],"antibiotic":[120],"resistance":[121],"genes,":[122],"virulence":[123],"genes":[124],"plasmids,":[126],"pangenome":[127],"construction":[128],"identification":[130],"nucleotide":[132],"variants.":[133],"All":[134],"results":[135],"are":[136],"processed":[137],"resumed":[139],"an":[141,162],"interactive":[142],"HTML":[143],"report":[144],"best":[146],"visualization":[148],"interpretation.":[150],"CONCLUSIONS:":[151],"minimal":[153],"user":[154],"intervention":[155],"makes":[158],"this":[160],"attractive":[163],"resource":[164],"microbiology":[166],"laboratories":[167],"with":[168],"no":[169],"expertise":[170],"first":[175],"line":[176],"method":[177],"typing":[180],"epidemiological":[182],"analyses,":[183],"that":[184],"would":[185],"help":[186],"reduce":[188],"costs":[190],"disease":[192],"outbreaks,":[193],"or":[194],"comparative":[196],"genomic":[197],"analyses.":[198],"publicly":[201],"available":[202],"https://github.com/JoseBarbero/CamPype":[204],".":[205]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
