- 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
- Pre/post surveys: 10 minutes
Order of tutorial
Please do the pre-learning quiz, then watch the presentation.
Once finished the tutorial, take the post-learing quiz.
Genomic Epidemiology And Strain Typing Pre-tutorial Survey
Presentation
Worksheets
Typing bacteria using MLST (via UNIX)
Typing bacteria using MLST (via Galaxy)
Undertaking genomic epidemiology using PopPUNK
Genomic Epidemiology And Strain Typing Post-tutorial Survey
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