- 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
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Binning and MAG generation
Rob Finn introduces the process of binning and MAG generation through the description of a large scale project to recover genomes from human gut metagenomic samples. This talk covers binning, assessment of completeness and contamination, bin refinement, dereplication of genomes, generation of MAG catalogues, and some considerations for eukaryotic genomes.
Practical
In this practical session you will have the chance to bin an assembly using MetaBAT2, assess the quality of the bins with checkM, and then visualise a placement of the bins/genomes within a reference tree.
All the necessary information you need for this practical can be found here in the MAG generation practical – https://mgnify-ebi-2020.readthedocs.io/en/latest/mag.html