MetaPro

MetaPro performs comprehensive processing and analysis of paired or single-end FASTQ metatranscriptomic and genomic sequence data to generate taxonomic assignments and global bacterial gene expression profiles.

Key Features:

• Scalability and Flexibility: Handles datasets comprising tens to hundreds of millions of sequence reads and supports incorporation of new algorithms.
• Cross-Platform Deployment: Implemented within a Docker container for consistent computational deployment across environments.
• Modular Architecture: Modular design enables integration of novel analytical algorithms.
• Comprehensive Data Processing: Performs tiered filtering, assembly, and annotation starting from raw FASTQ reads, including removal of low-quality sequences and potential contaminants.
• Taxonomic and Functional Annotation: Annotates processed reads with taxonomic and functional labels and produces consensus taxonomic predictions from complementary algorithms to derive global bacterial gene expression profiles.
• Enzyme Breakdown and Visualization: Conducts enzyme-level analyses with output compatible with Cytoscape network visualization.
• Benchmarked Performance: Performance has been benchmarked against state-of-the-art pipelines demonstrating superior functionality and efficiency.

Scientific Applications:

• Metatranscriptomic functional profiling: Identification and quantification of expressed microbial functions from environmental or host-associated communities using metatranscriptomic reads.
• Bacterial gene expression profiling: Generation of global bacterial gene expression profiles for comparative or temporal studies.
• Taxonomic composition analysis: Detailed taxonomic breakdowns using consensus predictions from complementary algorithms.
• Enzyme-centric network analysis: Enzyme activity breakdowns and network visualization in Cytoscape to interpret functional relationships.

Methodology:

Accepts paired or single-end FASTQ reads and applies quality filtering and contaminant removal, followed by assembly and annotation, consensus taxonomic prediction from complementary algorithms, generation of bacterial gene expression profiles, and enzyme-level analyses exportable to Cytoscape.