MGnify v6 released

EMBL-EBI’s microbiome derived sequence analysis resource MGnify has released version 6, a major update to the analysis infrastructure and the user-facing web resource. The latest version introduces updated analysis pipelines, a redesigned website and faster access to results at scale.

What’s new in MGnify?

MGnify v6 introduces major updates across its analysis pipelines, website and API, giving users richer annotations, improved marker-gene analysis and faster access to results at scale.

The assembly analysis pipeline now provides a broader set of annotations. These include biosynthetic gene cluster annotations, Rhea reactions, carbohydrate-active enzyme annotations from run_dbCAN, viral annotations using VIRify, mobile genetic element annotations using the Mobilome annotation pipeline, and DRAM summary outputs. Together, these additions give users a more detailed view of the biological functions, viruses and mobile elements present in assembled metagenomic datasets.

The amplicon analysis pipeline introduces amplicon sequence variants, or ASVs, which can provide higher taxonomic resolution than traditional operational taxonomic units. The pipeline now includes automatic detection of 16S and 18S marker genes, including identification of variable regions and primers using PIMENTO, a newly developed tool. Support for eukaryotic taxonomic assignments has been improved through the inclusion of PR2 as an additional reference database, alongside updates to existing tools and other reference databases. These changes support more precise and better-contextualised analysis of marker-gene datasets.

The raw-read analysis pipeline has also been updated. In addition to a more streamlined functional analysis, it includes taxonomic annotations using mOTUs. This analysis aims to complement the assembly-based analysis for samples where assembly is computationally demanding, for example for complex biomes such as soil, or where it is important to access rarer features in the community that can be missed in the assembly step.

Accessing MGnify data at scale

Alongside these pipeline updates, MGnify v6 introduces a redesigned website that makes it faster to search and browse studies, samples, analyses and associated results. New visualisations, including embedded MultiQC reports, allow users to inspect analysis results and quality statistics directly through the website.

Many of the website changes are designed to make it faster to preview the analysis results files before retrieving them for downstream analysis, and the release also features a new web API which provides faster programmatic access to MGnify data, with bulk result files hosted on high-speed EMBL-EBI infrastructure dedicated to file transfer.

This combination of updated pipelines, richer annotations and faster data access is intended to support the evolving needs of the microbiome research community. MGnify v6 users can work with more up-to-date annotations while accessing results in formats better suited to downstream computational workflows.