{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T08:41:57Z","timestamp":1775119317163,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,15]]},"abstract":"<jats:p>Summary: Advances in typing methodologies have recently reformed the field of molecular epidemiology of pathogens. The falling cost of sequencing technologies is creating a deluge of whole genome sequencing data that burdens bioinformatics resources and tool development. In particular, single nucleotide polymorphisms in core genomes of pathogens are recognized as the most important markers for inferring genetic relationships because they are evolutionarily stable and amenable to high-throughput detection methods. Sequence data will provide an excellent opportunity to extend our understanding of infectious disease when the challenge of extracting knowledge from available sequence resources is met. Here, we present an efficient and user-friendly genotype classification pipeline, CanSNPer, based on an easily expandable database of predefined canonical single nucleotide polymorphisms.<\/jats:p>\n               <jats:p>Availability and implementation: All documentation and Python-based source code for the CanSNPer are freely available at http:\/\/github.com\/adrlar\/CanSNPer.<\/jats:p>\n               <jats:p>Contact: \u00a0adrian.larkeryd@foi.se<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu113","type":"journal-article","created":{"date-parts":[[2014,2,27]],"date-time":"2014-02-27T01:26:41Z","timestamp":1393464401000},"page":"1762-1764","source":"Crossref","is-referenced-by-count":47,"title":["CanSNPer: a hierarchical genotype classifier of clonal pathogens"],"prefix":"10.1093","volume":"30","author":[{"given":"Adrian","family":"L\u00e4rkeryd","sequence":"first","affiliation":[{"name":"1 \u00a01Department of Clinical Microbiology, Ume\u00e5 University, 2Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, 3Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and 4Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kerstin","family":"Myrtenn\u00e4s","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Clinical Microbiology, Ume\u00e5 University, 2Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, 3Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and 4Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edvin","family":"Karlsson","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Clinical Microbiology, Ume\u00e5 University, 2Division of CBRN 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CBRN Security and Defence, FOI, Swedish Defence Research Agency, 3Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and 4Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"P\u00e4r","family":"Larsson","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Clinical Microbiology, Ume\u00e5 University, 2Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, 3Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and 4Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anders","family":"Johansson","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Clinical Microbiology, Ume\u00e5 University, 2Division 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