OH SFS Handbook
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Main page

  • About the OH SFS Handbook
  • License

Guidelines

  • EFSA and ECDC
  • International efforts

Sequencing technologies

  • Sequencing Technologies
  • Sequence file formats

Bioinformatics methods

  • Sequence analysis tool chains
  • Quality control and preprocessing
  • Data preprocessing
  • Data Production

Single isolate analysis

  • MLST
  • cgMLST
  • Serotyping
  • Virulence and AMR Detection

Cluster analysis

  • Clustering of xMLST data
  • SNPs and variant calling
  • Phylogenetic analysis

Compute Infrastructure

  • Storage and Compute Infrastructures
  • Workflow managers

Species analysis

  • Escherichia coli analysis
  • Campylobacter analysis
  • Salmonella analysis
  • Listeria monocytogenes analysis

Surveillance

  • Challenges for One Health surveillance

Contributing

  • How to contribute to this project
  • Contributors to this handbook
  • Contributor Covenant Code of Conduct
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