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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

This section explores quality control of raw shotgun data, its potential sources of contamination, how to identify low-quality sequences and adapters and how to filter data.

Quality control and host-decontamination – Lecture
Quality control and host-decontamination – Practical

Proceed through this section to view materials from all these sessions or select a specific session from the above list to jump ahead.

Genome-resolved metagenomics bioinformatics

Quality control and decontamination