Adrian Lärkeryd1, Kerstin Myrtennäs1, Edvin Karlsson1, Chinmay Kumar Dwibedi2, Mats Forsman1, Pär Larsson1, Anders Johansson1, Andreas Sjödin2. 1. Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden. 2. Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, SwedenDepartment of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden.
Abstract
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. AVAILABILITY AND IMPLEMENTATION: All documentation and Python-based source code for the CanSNPer are freely available at http://github.com/adrlar/CanSNPer.
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. AVAILABILITY AND IMPLEMENTATION: All documentation and Python-based source code for the CanSNPer are freely available at http://github.com/adrlar/CanSNPer.
Authors: C Schulze; K Heuner; K Myrtennäs; E Karlsson; D Jacob; P Kutzer; K GROßE; M Forsman; R Grunow Journal: Epidemiol Infect Date: 2016-06-30 Impact factor: 4.434
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Authors: Ingmar Janse; Rozemarijn Q J van der Plaats; Ana Maria de Roda Husman; Mark W J van Passel Journal: Front Cell Infect Microbiol Date: 2018-05-08 Impact factor: 5.293