- Course overview
- Search within this course
- Introduction
- Course materials and software
- Metagenomics bioinformatics – course introduction
- Quality control and host decontamination
- The European Nucleotide Archive
- Tools to assemble short reads
- MGnify services
- MGnifyR
- Binning and MAG generation
- ENA metagenomics standards
- MGnify MAG resources
- Strain resolution
- Tools for comparative metagenomics
- Your feedback
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Strain resolution
Chris Quince from the Earlham Institute discusses the process of resolving strains information from metagenomic data. This talk covers the process of de novo strain resolution, and highlights two different tools that can be used in this process, DESMAN and STRONG.
Practical
You can learn about the process of de novo strain resolution as outlined by Chris Quince in the practical presented below from Sebastien Raguideau. You will need to download and install STRONG on your own machine to run this practical. Information on how to do so is included in the README file.
If you are interested in scaling-up your analyses or want to create a reproducible workflow, then follow the Snakemake practical tutorial.