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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

Quality control and decontamination – Lecture

Overview: This talk will explore the quality control of raw shotgun data – looking at potential sources of contamination and methods to identify low quality sequences and adapters.

Learning objectives:

After this session you should be able to:

Describe the importance and different steps involved in:

Visualising general quality statistics
Read trimming
Removal of sequence artifacts
Host decontamination

Materials: Presentation

Genome-resolved metagenomics bioinformatics

Quality control and decontamination – Lecture