- Course overview
- Search within this course
- Introduction
- Course materials and software
- Metagenomics bioinformatics – course introduction
- Quality control and host decontamination
- The European Nucleotide Archive
- Tools to assemble short reads
- MGnify services
- MGnifyR
- Binning and MAG generation
- ENA metagenomics standards
- MGnify MAG resources
- Strain resolution
- Tools for comparative metagenomics
- Your feedback
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Introduction
This online course ran virtually between 2-6 November 2020. The lecture sessions were recorded and have been made available here along with the practical exercise guides. A full overview of the live course, including the programme, can be found here.
Topics covered in this online tutorial include:
- Microbiome data types:
- Amplicon approaches (ribosomal RNA)
- Whole-genome shotgun (WGS) approaches
- Assembly and metagenome-assembled genomes (MAGs)
- MAG generation workflow:
- Quality control and decontamination
- Assembly of short-reads
- Binning of assemblies
- Metagenomics data analysis:
- taxonomic analysis
- functional analysis
- strain resolution
- comparative analysis
- Data standards and submission: