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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 -practical

Overview: In this practical you will perform quality control on some examples of short read metagenomic data using the concepts discussed in the previous lecture. We will visualise quality statistics, filter reads or contigs and understand the importance of experimental controls.

Learning objectives:

After this session you should be able to:

Visualise general quality statistics
Perform basic read trimming of NGS datasets
Remove sequence artifacts
Perform host decontamination

Materials: Practical

Genome-resolved metagenomics bioinformatics

Quality control and decontamination -practical