baseLess

baseLess detects specific nucleotide sequences directly from raw electrical signals produced by Oxford Nanopore Technologies' MinION to enable target sequence identification without base-calling.

Key Features:

• Target-Detection-Only Analysis: Focuses exclusively on identifying target sequences from raw MinION electrical signal, bypassing base-calling to reduce computational requirements.
• Neural Network Architecture: Employs an array of small neural networks, each specialized to recognize a fixed-size subsequence (k-mer) directly from the electrical signal, and composes sequence detections by combining these networks.
• Cost-Effective Deployment: Designed for execution on low-cost computational hardware such as single-board computers, reducing the need for high-end computing resources.
• Accuracy and Versatility: Empirically validated to distinguish closely related organisms (three fish species) and to classify sequences from mixtures of 20 bacterial species.

Scientific Applications:

• Infectious Disease Monitoring: Enables targeted detection of pathogen sequences from MinION signal data for surveillance applications.
• Species Identification: Detects species-specific sequences for taxonomic identification, including discrimination of closely related fish species.
• Environmental Monitoring: Supports detection of target DNA in environmental samples for biodiversity assessments and field-based studies.
• Real-time Genomic Surveillance: Facilitates rapid on-site detection and decision-making by identifying target sequences directly from electrical signals.

Methodology:

Analyzes raw MinION electrical signal using arrays of small neural networks that detect fixed-size k-mers directly and combine k-mer detections to identify target sequences without performing base-calling.