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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

Tools to assemble short- and long- reads: lecture

Overview: In this section, you will be introduced to the basic concepts of metagenome assembly. We will cover the main algorithms behind the process, and describe some of the tools commonly used for assembling both short- and long-read data, as well as some common considerations and pitfalls.

Learning outcomes

After this session you should be able to:

Identify the main sequencing technologies used for metagenomics data generation
Identify the main algorithms used for assembling metagenomics sequencing reads
Identify different computational resources and tools available for assembly in metagenomics analysis
Identify different characteristics of assembly and co-assembly

Materials: Presentation

Genome-resolved metagenomics bioinformatics

Tools to assemble short- and long- reads: lecture