- 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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MGnify MAG resources
Martin Beracochea, from EMBL-EBI, introduces the MAG resources available at MGnify as well as how you can use the MGnify API. This talk covers searching and browsing the Unified Human Gastrointestinal Genome (UHGG) catalogue, how the contig viewer works, what annotations are included, and how you can search the UHGG with short sequences. Martin also provides a brief overview of the MGnify API and its documentation.
Practical
You can access this practical in the MGnify Read the Docs resource. You will need to install the Conda software package and create a working directory, as detailed in the tutorial, to be able to fully work through this practical.
- Practical guide: MGnify Read the Docs
The links below might be useful to you in taking the next steps with MGnify and conducting your metagenomics analysis:
- MGnify API documentation: https://emg-docs.readthedocs.io/en/latest/api.html
- MG-Toolkit: https://pypi.org/project/mg-toolkit/
- JSON API specs: https://jsonapi.org/format/
- JSON API implementations: https://jsonapi.org/implementations/
- API – https://www.ebi.ac.uk/metagenomics/api.docs