title: CanSNPer: a hierarchical genotype classifier of clonal pathogens.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  All documentation and Python-based source code for the CanSNPer are freely available at http://github.com/adrlar/CanSNPer.
authors.affiliation: 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.
authors.forename: Adrian
authors.initials: A
authors.lastname: Lärkeryd
authors.affiliation: 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.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Myrtennäs
authors.affiliation: 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.
authors.forename: Edvin
authors.initials: E
authors.lastname: Karlsson
authors.affiliation: 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.
authors.forename: Chinmay Kumar
authors.initials: CK
authors.lastname: Dwibedi
authors.affiliation: 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.
authors.forename: Mats
authors.initials: M
authors.lastname: Forsman
authors.affiliation: 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.
authors.forename: Pär
authors.initials: P
authors.lastname: Larsson
authors.affiliation: 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.
authors.forename: Anders
authors.initials: A
authors.lastname: Johansson
authors.affiliation: 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.
authors.forename: Andreas
authors.initials: A
authors.lastname: Sjödin
mesh_terms: D023281:Genomics / Q000379:methods; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D058889:Molecular Typing / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software