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  • Technical Descriptions of Analysis Tools
    • Genome Assembly
      • Short Read Assembly
      • Assembling genomes with EToKi
    • Plasmid Annotation
      • Inctyper
    • Assigning species with Speciator
    • Trees, Clustering, and Context Search
      • Core Genome Tree
        • About SNP-based trees
        • Core Assignment
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      • Genotyphi
      • Kleborate
      • cgMLST
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      • MLST
      • NG-MAST
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      • PopPUNK
      • Vista
      • Finding HierCC codes with hclink
      • SARS-CoV-2 Notable Mutations
    • Serotyping
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  • WHO bacterial priority pathogens
  • Initiatives powered by Pathogenwatch
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      • What is the PATH-SAFE Programme?
      • PATH-SAFE powered by Pathogenwatch
      • Two-tool Serotyping with SISTR & SeqSero2
      • S. enterica SNP tree
      • PATH-SAFE analyses
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  1. Technical Descriptions of Analysis Tools

Lineage Assignment & Genotyping Methods

PreviouscgMLST TreeNextGenotyphi

Last updated 3 months ago

Genotyphi
Kleborate
cgMLST
Klebsiella LIN Codes
MLST
NG-MAST
Pangolin
PopPUNK
Vista
Finding HierCC codes with hclink
SARS-CoV-2 Notable Mutations