MGnify: the microbiome sequence data analysis resource in 2023

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• The MGnify platform is a comprehensive resource for microbiome sequence data analysis and archiving.
• It currently hosts nearly half a million analyses across various environments and sequencing types (metabarcoding, metatranscriptomics, metagenomics).

Purpose of the Study:

• To detail recent advancements and expanded capabilities of the MGnify platform.
• To highlight improvements in data organization, annotation depth, and user accessibility for microbiome research.

Main Methods:

• Expansion of the MGnify protein database to over 2.4 billion non-redundant sequences.
• Implementation of deep learning methods for advanced functional annotation.
• Upgrade of the platform's website and Application Programming Interface (API).
• Integration of a Jupyter Lab environment for downstream data analysis.

Main Results:

• The MGnify protein database is now organized into a relational database, enabling navigation of genomic context.
• Deep learning-based annotations have been applied, extending functional insights beyond previous capabilities.
• The platform now supports analysis of long-read sequences.
• Users can now perform downstream analyses directly within the MGnify ecosystem.

Conclusions:

• MGnify has significantly evolved, offering a more powerful and integrated environment for microbiome data exploration.
• The platform's advancements facilitate deeper understanding of microbial communities through improved data accessibility and analytical tools.