MetaLAFFA

MetaLAFFA generates functional profiles from shotgun metagenomic sequencing data to characterize the aggregate functional potential of microbial communities.

Key Features:

• End-to-End Pipeline: Processes unfiltered shotgun metagenomic data from raw FASTQ files (with sequencing adapters removed) to produce functional profiles.
• Distributed Computing Compatibility: Implemented as a Snakemake pipeline and compatible with distributed computing clusters.
• Flexible Customization: Provides default settings and a Python module-based configuration system for user customization.
• Quality Assurance: Generates summary statistics at each pipeline step to assess preprocessing and annotation quality.

Scientific Applications:

• Functional profiling of microbial communities: Identifies aggregate functional capacities encoded by microbial communities from shotgun metagenomes, supporting research in microbiology, ecology, and environmental science.

Methodology:

The pipeline begins with raw FASTQ files, processes them through several stages, and outputs functional profiles based on orthologous groups.