MUFFIN

MUFFIN integrates short- and long-read sequencing to reconstruct high-quality metagenome-assembled genomes (MAGs) and profile the taxonomic and functional potential of microbial communities.

Key Features:

• Hybrid short- and long-read integration: Integrates short- and long-read sequencing data to improve metagenome assembly and reduce MAG fragmentation.
• Genome reconstruction: Performs hybrid assembly to produce high-quality metagenome-assembled genomes (MAGs).
• Differential coverage binning: Implements differential coverage binning to separate genomes within metagenomic samples.
• Taxonomic classification: Assigns taxonomy to assembled bins.
• KEGG pathway analysis: Predicts functional potential of bins using KEGG pathway annotations.
• RNA-Seq integration: Incorporates RNA-Seq data for transcript quantification and de novo transcript annotation across metagenomic samples.
• Workflow orchestration: Orchestrated with Nextflow to ensure reproducible execution of computational steps.
• Output generation: Produces files required for microbial community analysis and functional assessment.

Scientific Applications:

• Metagenome-assembled genome recovery: Reconstruction of high-quality MAGs from metagenomic datasets using hybrid sequencing.
• Genome bin separation and annotation: Separation and annotation of individual genomes within complex metagenomic samples via differential coverage binning.
• Taxonomic profiling: Determination of microbial community composition through taxonomic classification of bins.
• Functional potential inference: KEGG-based pathway prediction to assess metabolic capabilities of community members.
• Transcriptomic analysis within metagenomes: Quantification and de novo annotation of transcripts from RNA-Seq integrated with metagenomic assemblies.
• Environmental application example: Applied to twenty biogas reactor samples for community and functional assessment.

Methodology:

Nextflow orchestrates a workflow that integrates short- and long-read sequencing for hybrid assembly and genome reconstruction, applies differential coverage binning, performs taxonomic classification and KEGG pathway analysis, and optionally incorporates RNA-Seq for transcript quantification and de novo annotation, producing files for microbial community and functional analysis.