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CanSNPer: a hierarchical genotype classifier of clonal pathogens
Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency.
Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency.
Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Bacteriology. Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency. (Anders Johansson)
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2014 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 30, no 12, 1762-1764 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Oxford University Press, 2014. Vol. 30, no 12, 1762-1764 p.
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:umu:diva-91378DOI: 10.1093/bioinformatics/btu113ISI: 000338109200055OAI: oai:DiVA.org:umu-91378DiVA: diva2:736540
Available from: 2014-08-07 Created: 2014-08-04 Last updated: 2017-12-05Bibliographically approved

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Lärkeryd, AdrianMyrtennäs, KerstinDwibedi, Chinmay KumarSjödin, Andreas

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Lärkeryd, AdrianMyrtennäs, KerstinDwibedi, Chinmay KumarJohansson, AndersSjödin, Andreas
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Department of Clinical MicrobiologyClinical BacteriologyMolecular Infection Medicine Sweden (MIMS)Department of Chemistry
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