Course content

The contents table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainer. Either proceed through the materials using the arrows at the end of each page or pick your topic of interest from the table below to skip straight to it.

To see details about the live Genome-resolved metagenomics bioinformatics course and the original programme, you can refer to the course page and programme.

 Presentation slides –  View or download the slides

 Recorded lectures – Watch the lecture videos 

 Practicals – View or download the slides, exercises, datasets, analysis scripts and results

Format	Subject	Trainer
	Course introduction
	Course introduction	Lorna Richardson
	Experimental design
	Experimental considerations of metagenomics	Vladimir Benes
	Quality control and decontamination
	Quality control and host-decontamination – Lecture	Varsha Kale
	QC & decontamination – Practical	Varsha Kale
	Assembly and annotation
	Tools to assemble short- and long- reads: lecture	Juan Caballero
	Assembly and co-assembly: practical	Juan Caballero and Tanya Gurbich
	Introduction to Viral Annotations: practical	Varsha Kale
	Binning and MAG generation
	Binning and MAG generation: lecture	Tanya Gurbich
	Binning and MAG generation: practical	Tanya Gurbich
	The European Nucleotide Archive – ENA
	European Nucleotide Archive – Lecture	Maira Ihsan
	ENA Metagenomics Standards and MAG layer: lecture	Maira Ihsan and Josephine Burgin
	The MGnify services and resources
	MGnify MAG resources: lecture	Sandy Rogers
	Programmatic access to MGnify resources with APIs and notebooks: practical	Sandy Rogers
	Strain Resolution
	Strain resolution – Lecture	Chris Quince
	Strain resolution – Practical	Sebastien Raguideau
	Comparative metagenome analysis
	Comparative metagenome analysis – Lecture	Jennifer Lu and Alejandra Escobar-Zepeda
	Comparative metagenome analysis – Practical	Jennifer Lu and Alejandra Escobar-Zepeda