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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

Binning and MAG generation: practical

Overview: In the practical session you will have the chance to assemble short-read metagenomic data into contigs, perform basic analysis of assembled data, bin an assembly using MetaBAT2, assess the quality of the bins with checkM, and then visualise a placement of the bins/genomes within a reference tree.

Learning outcomes

After this session you should be able to:

Identify the usefulness of MAGs
Identify the main algorithms employed to generate MAGs
Perform assessment of MAG quality, taxonomic assignment, and dereplication of MAGs across samples
Use MAGs to create the Unified Human Gastrointestinal Genome (UHGG) collection

Materials:

Practical

Genome-resolved metagenomics bioinformatics

Binning and MAG generation: practical