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 https://www.ebi.ac.uk/training/events/metagenomics-bioinformatics-mgnify/.

 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

FormatSubjectTrainer
Introductory lectures
Course introductionSandy Rogers and Varsha Kale
European Nucleotide Archive: ENA submissionMaira Ihsan, Germana Baldi, and Josephine Burgin
Experimental design
Experimental considerations of metagenomicsVladimir Benes
Quality control and decontamination
QC and decontamination: lectureJennifer Lu and Christian Atallah

QC and decontamination: practicalJennifer Lu, Christian Atallah and Varsha Kale
Assembly and annotation
Assembly and co-assembly: lectureGermana Baldi

Assembly and co-assembly: practicalGermana Baldi, Sonya Ochkalova, and Tatiana Gurbich

Functional and taxonomic annotationChristian Atallah

Mobilome annotationAlejandra Escobar-Zepeda

Introduction to viral annotations: practicalGuillermo Rangel Piñeros and Varsha Kale
Comparative metagenomics
Comparative metagenomics: lectureAlejandra Escobar-Zepeda

Comparative metagenomics: practicalAlejandra Escobar-Zepeda and Christian Atallah
Metagenome Assembled Genomes (MAGs)

MAG generation: lectureTanya Gurbich and Ekaterina Sakharova

MAG generation: practicalTanya Gurbich and Ekaterina Sakharova

MAG submissionJosephine Burgin and Maira Ihsan

MAG catalogues as a resourceMahfouz Shehu and Sandy Rogers
MGnifyR and miaverseLeo Lahti and Tuomas Borman
Microbial strainsJethro Johnson and Avery Robinson
Pan-genomes and subspecies
Pan-genomes and subspecies practicalJohn Lees, Samuel Horsfield, Joel Hellewell, Leonie Lorenz and Jacqueline Toussaint, Johanna Helene von Wachsmann
Looking forward: New developments & applicationsSusheel Bhanu Busi