DecontaMiner

DecontaMiner identifies and analyzes contaminating microbial sequences in unmapped Next-Generation Sequencing (NGS) reads to detect exogenous bacteria, fungi, and viruses and assess potential contamination sources.

Key Features:

• Subtraction Approach: Employs a subtraction methodology on unmapped reads to detect genome contamination from bacteria, fungi, and viruses.
• Output Files: Produces output files that track processed reads, quantify high-quality matches to microorganism genomes, and enable comparative analysis across samples.
• Summary Statistics and Plots: Generates summary statistics and visual plots representing contamination levels and match characteristics.
• Automated Pipeline: Provides an automated pipeline compatible with standard NGS workflows for systematic contamination analysis.

Scientific Applications:

• Human RNA-Seq contamination detection: Applied to human RNA-Seq datasets to detect contaminating organisms and support validation of experimental results.
• NGS quality control and artifact discrimination: Identifies potential contaminants to help distinguish genuine biological signals from artifacts introduced during sample preparation or sequencing.

Methodology:

Processes unmapped NGS reads using a subtraction approach to identify sequences matching known bacterial, fungal, and viral genomes and quantifies high-quality matches.