MuDoGeR

MuDoGeR recovers Metagenome-Assembled Genomes (MAGs) and uncultivated viral genomes from whole-genome shotgun (WGS) metagenomic samples to enable multi-domain genomic analyses.

Key Features:

• Multi-domain genome recovery: Recovers genomes from prokaryotes, eukaryotes, and viruses, including Metagenome-Assembled Genomes (MAGs) and uncultivated viral genomes (UViGs).
• Wrapper integration: Orchestrates multiple computational tools into unified workflows for genome recovery and downstream analysis.
• Annotation: Produces genome annotations for recovered MAGs and viral genomes.
• Dereplication: Performs dereplication to generate non-redundant genome sets.
• Taxonomy assignment: Assigns taxonomic labels to recovered genomes.
• Abundance and coverage estimation: Computes relative abundance and coverage metrics across recovered genomes and domains.
• Viral characterization focus: Characterizes bacterial and archaeal viruses primarily while retaining the ability to recover eukaryotic viral sequences.
• Validation: Has been tested on datasets including 24 individual isolated genomes and 574 metagenomes.
• Output generation: Produces assembled genomes and associated analysis outputs (annotations, dereplicated sets, taxonomy assignments, abundance and coverage tables).

Scientific Applications:

• Microbial ecology: Enables analysis of microbial community composition and interactions through recovered prokaryotic and eukaryotic genomes.
• Virology: Facilitates discovery and characterization of bacterial, archaeal, and eukaryotic viruses from metagenomes.
• Environmental genomics: Supports studies of biodiversity and functional potential in environmental metagenomic samples.
• Large-scale genomic surveys: Applies to high-throughput projects and biodiversity assessments requiring multi-domain genome recovery and abundance estimation.

Methodology:

Wraps and executes multiple computational tools to recover MAGs and uncultivated viral genomes from WGS metagenomic samples and to perform annotation, dereplication, taxonomic assignment, and calculation of relative abundance and coverage.