MGnify

MGnify provides assembly, taxonomic and functional analysis, and archiving of microbiome sequencing datasets to characterize microbial taxa, protein functions, and biochemical pathways from metagenomic contigs.

Key Features:

• Multiple Analysis Pipelines: Version 5.0 replaces a single pipeline with multiple tailored pipelines to accommodate different input data types.
• Common Workflow Language (CWL): Pipelines are formally described using the Common Workflow Language to capture provenance and enable reproducibility.
• ITS1/2 Taxonomic Assertions: Taxonomic assignment uses ribosomal internal transcribed spacer regions (ITS1/2) for improved taxonomic resolution.
• Expanded Protein Functional Annotations: Protein sequences derived from assemblies receive expanded functional annotation.
• Biochemical Pathways and Systems Predictions: Predictions of biochemical pathways and systems are produced for assembled contigs.
• Enhanced Metagenomic Assembly: Focused metagenomic assembly has increased the number of assembled datasets approximately six-fold.
• Non-redundant Protein Database: A non-redundant protein database constructed from assemblies contains over 1 billion sequences.
• Contig Visualization: A contig viewer provides visualization of assembled contigs together with enriched annotations.

Scientific Applications:

• Taxonomic profiling (ITS1/2): Assignment of taxa using ribosomal ITS1/2 regions to characterize microbial community composition.
• Protein functional annotation and cataloguing: Annotation of protein sequences and construction of a non-redundant protein catalogue from metagenomic assemblies.
• Metabolic and systems prediction: Inference of biochemical pathways and systems from assembled contigs to assess microbial functions and interactions.
• Metagenome assembly and gene discovery: Assembly of metagenomic datasets to recover contigs and associated gene content across environmental samples.
• Exploration of community structure and function: Visualization and annotation of contigs to investigate the detailed structure and functional potential of microbial communities.

Methodology:

Version 5.0 implements multiple tailored analysis pipelines formalized in the Common Workflow Language; methods explicitly include metagenomic assembly, taxonomic assignment using ITS1/2, expanded protein functional annotation, prediction of biochemical pathways and systems on assembled contigs, and construction of a non-redundant protein database (>1 billion sequences) from assemblies.