EMBL-EBI
Course materials, Slidedeck
Using MGnify as the marine microbiome data hub for BlueRemediomics
MGnify (https://www.ebi.ac.uk/metagenomics) ran a two-part training course in association with the BlueRemediomics General Assembly in 2025. These materials cover the content of that course. Sessions 1-3 are suitable for those unfamiliar with bioinformatics. Session 4-5 require some understanding of bioinformatics.
Licence: Creative Commons Zero v1.0 Universal
Contact: https://www.ebi.ac.uk/about/contact/support/metagenomics
Keywords: Microbiome, Analysis pipeline, Metagenome-Assembled Genome (MAG), Metagenomics, Protein sequence databases, protein sequence analysis, metatranscriptomics, Metabarcoding, Bioinformatic analysis, Bioinformatic databases
Resource type: Course materials, Slidedeck
Status: Archived
Prerequisites:
Sessions 1-3: No prerequisites.
Sessions 3-4: Suitable for those familiar with bioinformatics.
Learning objectives:
Introductory course (sessions 1-3)
- Identify and describe the different types of sequencing analysis annotations hosted on MGnify
- Demonstrate browsing and searching for annotations on the MGnify website
- Use the MGnify Proteins resource to search for a protein sequence and interrogate the resulting matches
- Navigate around a MGnifams entry and perform a search against Pfam
- Explain the process of MAG- and catalogue-generation within MGnify
- Use the MGnify Genomes resource to compare a gene or a genome against the existing catalogues
Advanced course (sessions 4-5)
- Programmatically access MGnify data through the MGnify API
- Use Jupyter Notebooks to perform downstream analysis and data manipulation using MGnify data
Date created: 2025-04-16
Date modified: 2025-05-30
Date published: 2025-06-10
Contributors: MGnify team
Scientific topics: Metagenomics, Bioinformatics, Protein sites, features and motifs, Metabarcoding, Metatranscriptomics, Workflows
Activity log
