- This tutorial outlines the basics concepts in undertaking clustering and typing of bacterial strains
Learning outcomes
- State the different levels at which bacterial typing occurs
- Explain the basis of ANI and MLST for species and strain typing
- State the differences between MLST and cgMLST in terms of resolution and use
- Recognise MinHash and MST approaches for genomic epidemiology
- Implement the MLST and PopPUNK tools for undertaking typing and clustering
Prerequisites
- It is recommended that you have Notepad++ (Windows) or BBEdit (Mac) for viewing fasta files; most linux default editors can do this.
- It is recommended that you have followed the Concepts in Computer Programming, UNIX tutorial (basics) and Setting up and using conda tutorials if you are going to do the UNIX-based worksheets.
Approximate time to finish tutorial
- Lecture: 30 mins
- Tutorials: 30 mins
Presentation
During the presentation there are points to stop and do exercises, which are linked below. The answers to the questions in the exercises are linked within each one.
Worksheets
Typing bacteria using MLST (via UNIX)
Typing bacteria using MLST (via Galaxy)
Undertaking genomic epidemiology using PopPUNK
Other tutorials/tools
- Sourmash for assigning samples to clusters and typing strains at species and sub-species levels
- Introduction to MLST as it applies to E. coli
- Grapetree for building minimum spanning trees for any alellic information