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Course content
Course introduction
Experimental considerations of metagenomics
Quality control and decontamination
- Quality control and decontamination – Lecture
- Quality control and decontamination -practical
Assembly and annotation
Binning and MAG generation
- Binning and MAG generation: lecture
- Binning and MAG generation: practical
The European Nucleotide Archive – ENA
- The European Nucleotide Archive – Lecture
- ENA Metagenomics Standards and MAG layer – Lecture
MGnify MAG resources
- MGnify MAG resources: lecture
- Programmatic access to MGnify resources with APIs and notebooks: practical
Strain resolution
- Strain resolution – Lecture
- Strain resolution – Practical
Comparative metagenome analysis
- Comparative metagenome analysis – Lecture
- Comparative metagenome analysis with MGnifyR – Practical
Technical Help sheet
Trainer biographies
Further learning
Your feedback

Strain resolution – Practical

Overview:

Overview: In this session we will learn how to use the STRONG pipeline, precisely in which way we can characterise strain diversity and dynamic from metagenomic datasets. The practical will be carried out on a reduced dataset from anaerobic digestor.

Learning outcomes:

After this session you should be able to:

Perform strain resolution on assembly graphs – STRONG
Describe validation and exploratory results from long reads

Materials:

Practical
STRONG-0.0.1-beta

Genome-resolved metagenomics bioinformatics

Strain resolution – Practical