CoMW

CoMW performs assembly-based functional classification and quantification of mRNA reads from next-generation sequencing (NGS) short-read metatranscriptomic and total RNA studies to profile microbial community activities.

Key Features:

• De-novo Assembly-Based Approach: Employs de-novo assembly of short reads into contigs prior to alignment to reference databases.
• Quality Filtering: Performs initial processing to ensure high-quality mRNA reads.
• Alignment and Annotation: Aligns assembled contigs to reference databases for functional annotation.
• Quantification: Quantifies gene expression levels from contigs while minimizing false positives.
• Improved Precision and Recall: Benchmarked against assembly-free workflows on simulated and real-world metatranscriptomes from Arctic and Temperate terrestrial environments, showing significantly higher precision and reduced false positives.
• Comprehensive Database Utilization: Uses databases including M5nr, Carbohydrate Active-enzyme, and Nitrogen Cycle for functional annotation, reporting a 0.6% false positive rate with M5nr and identifying genes with 3-5 times fewer false positives in specialized databases compared to assembly-free methods.
• Modular and Reproducible Structure: Implements a modular workflow structure to support reproducible analysis across datasets.

Scientific Applications:

• Metatranscriptomic Functional Profiling: Enables accurate functional classification and quantification of expressed genes in metatranscriptomic and total RNA datasets.
• Environmental Microbial Ecology: Supports analysis of microbial community dynamics and ecological responses to environmental stimuli in Arctic and Temperate terrestrial systems.

Methodology:

The workflow includes quality filtering of mRNA reads, de-novo assembly of short reads into contigs, alignment of contigs to reference databases for functional annotation, and quantification of gene expression levels.