{"id":"https://openalex.org/W2950050732","doi":"https://doi.org/10.1093/bioinformatics/bty212","title":"SnapperDB: a database solution for routine sequencing analysis of bacterial isolates","display_name":"SnapperDB: a database solution for routine sequencing analysis of bacterial isolates","publication_year":2018,"publication_date":"2018-04-04","ids":{"openalex":"https://openalex.org/W2950050732","doi":"https://doi.org/10.1093/bioinformatics/bty212","mag":"2950050732","pmid":"https://pubmed.ncbi.nlm.nih.gov/29659710"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty212","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/3028/25703020/bty212.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/3028/25703020/bty212.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078986035","display_name":"Timothy J. Dallman","orcid":"https://orcid.org/0000-0001-7105-2543"},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Timothy Dallman","raw_affiliation_strings":["Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"],"affiliations":[{"raw_affiliation_string":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033397472","display_name":"Philip Ashton","orcid":"https://orcid.org/0000-0002-1545-9661"},"institutions":[{"id":"https://openalex.org/I4210150114","display_name":"Oxford University Clinical Research Unit","ror":"https://ror.org/05rehad94","country_code":"VN","type":"facility","lineage":["https://openalex.org/I40120149","https://openalex.org/I4210150114","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB","VN"],"is_corresponding":false,"raw_author_name":"Philip Ashton","raw_affiliation_strings":["Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK","Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam"],"affiliations":[{"raw_affiliation_string":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]},{"raw_affiliation_string":"Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I4210150114"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049364601","display_name":"Ulf Schafer","orcid":null},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ulf Schafer","raw_affiliation_strings":["Infectious Disease Informatics, National Infections Service, Public Health England, London, UK"],"affiliations":[{"raw_affiliation_string":"Infectious Disease Informatics, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048297020","display_name":"Aleksey Jironkin","orcid":"https://orcid.org/0000-0002-5450-0479"},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Aleksey Jironkin","raw_affiliation_strings":["Infectious Disease Informatics, National Infections Service, Public Health England, London, UK"],"affiliations":[{"raw_affiliation_string":"Infectious Disease Informatics, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008819822","display_name":"Ana\u00efs Painset","orcid":"https://orcid.org/0000-0003-3569-6530"},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anais Painset","raw_affiliation_strings":["Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"],"affiliations":[{"raw_affiliation_string":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083576939","display_name":"Sharif Shaaban","orcid":"https://orcid.org/0000-0001-8293-9481"},"institutions":[{"id":"https://openalex.org/I133960621","display_name":"Roslin Institute","ror":"https://ror.org/01920rj20","country_code":"GB","type":"facility","lineage":["https://openalex.org/I133960621","https://openalex.org/I2799693246","https://openalex.org/I4210087105","https://openalex.org/I98677209"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sharif Shaaban","raw_affiliation_strings":["Roslin Institute, University of Edinburgh, Scotland, UK"],"affiliations":[{"raw_affiliation_string":"Roslin Institute, University of Edinburgh, Scotland, UK","institution_ids":["https://openalex.org/I133960621","https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002845291","display_name":"Hassan Hartman","orcid":"https://orcid.org/0000-0003-0019-1364"},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Hassan Hartman","raw_affiliation_strings":["Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"],"affiliations":[{"raw_affiliation_string":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062024371","display_name":"Richard Myers","orcid":"https://orcid.org/0000-0003-4269-1164"},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard Myers","raw_affiliation_strings":["Infectious Disease Informatics, National Infections Service, Public Health England, London, UK"],"affiliations":[{"raw_affiliation_string":"Infectious Disease Informatics, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033697975","display_name":"Anthony Underwood","orcid":"https://orcid.org/0000-0002-8547-4277"},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anthony Underwood","raw_affiliation_strings":["Infectious Disease Informatics, National Infections Service, Public Health England, London, UK"],"affiliations":[{"raw_affiliation_string":"Infectious Disease Informatics, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037140433","display_name":"Claire Jenkins","orcid":"https://orcid.org/0000-0001-8600-9169"},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Claire Jenkins","raw_affiliation_strings":["Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"],"affiliations":[{"raw_affiliation_string":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114015631","display_name":"Kathie Grant","orcid":null},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kathie Grant","raw_affiliation_strings":["Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"],"affiliations":[{"raw_affiliation_string":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK","institution_ids":["https://openalex.org/I348769827"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5078986035"],"corresponding_institution_ids":["https://openalex.org/I348769827"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":9.4023,"has_fulltext":true,"cited_by_count":222,"citation_normalized_percentile":{"value":0.98727206,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"34","issue":"17","first_page":"3028","last_page":"3029"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9984999895095825,"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/T10066","display_name":"Gut microbiota and health","score":0.996999979019165,"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/computer-science","display_name":"Computer science","score":0.496467649936676},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.487298846244812},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3538168668746948},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24635162949562073}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.496467649936676},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.487298846244812},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3538168668746948},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24635162949562073}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty212","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/3028/25703020/bty212.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29659710","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29659710","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:pure.ed.ac.uk:publications/0a7004f8-e3af-4fdc-a073-6d0c91395ec1","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/0a7004f8-e3af-4fdc-a073-6d0c91395ec1","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Dallman, T, Ashton, P, Schafer, U, Jironkin, A, Painset, A, Shaaban, S, Hartman, H, Myers, R, Underwood, A, Jenkins, C & Grant, K 2018, 'SnapperDB: A database solution for routine sequencing analysis of bacterial isolates', Bioinformatics, vol. 34, no. 17, pp. 3028-3029. https://doi.org/10.1093/bioinformatics/bty212","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty212","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/3028/25703020/bty212.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":null,"license_id":null,"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/F4320309229","display_name":"National Institute on Handicapped Research","ror":null},{"id":"https://openalex.org/F4320318095","display_name":"National Institute for Health Research Health Protection Research Unit","ror":null},{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320319994","display_name":"Department of Health and Social Care","ror":"https://ror.org/03sbpja79"},{"id":"https://openalex.org/F4320321067","display_name":"Public Health England","ror":"https://ror.org/00vbvha87"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2950050732.pdf","grobid_xml":"https://content.openalex.org/works/W2950050732.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1972145956","https://openalex.org/W2097318327","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2119180969","https://openalex.org/W2170551349","https://openalex.org/W2181779082","https://openalex.org/W2326037388","https://openalex.org/W2396762411","https://openalex.org/W2420476773","https://openalex.org/W2542103377","https://openalex.org/W2715387098","https://openalex.org/W4247053599"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"SnapperDB":[0,25],"is":[1],"implemented":[2],"as":[3],"a":[4],"python":[5],"application":[6],"under":[7],"the":[8],"open":[9],"source":[10],"BSD":[11],"license.":[12],"All":[13],"code":[14],"and":[15,24],"user":[16],"guides":[17],"are":[18,27],"available":[19,28],"at":[20,29],"https://github.com/phe-bioinformatics/snapperdb.":[21],"Reference":[22],"genomes":[23],"configs":[26],"https://github.com/phe-bioinformatics/snapperdb_references.":[30]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":26},{"year":2024,"cited_by_count":37},{"year":2023,"cited_by_count":29},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":37},{"year":2020,"cited_by_count":35},{"year":2019,"cited_by_count":21},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":1}],"updated_date":"2026-04-19T08:26:33.389920","created_date":"2025-10-10T00:00:00"}
