DeepNano-blitz

DeepNano-blitz performs real-time base calling of Oxford Nanopore MinION sequencing signal to generate nucleotide sequences on CPU-only systems for rapid in-situ genomic analysis.

Key Features:

• Real-time multi-run processing: Processes sequencing data in real time from up to two MinION runs concurrently.
• CPU-only operation: Executes base calling on a standard laptop CPU without requiring a GPU.
• Hardware tested: Performance validated on an Intel i7-7700HQ processor.
• Adjustable accuracy–speed trade-off: Provides configurable base caller settings to balance accuracy and processing speed.
• Run-time monitoring: Enables monitoring of sample composition, barcode balance, and species identification during sequencing runs.
• Pre-filtering capabilities: Supports filtering of reads such as removal of human DNA in mixed human–pathogen samples.

Scientific Applications:

• Environmental monitoring: Facilitates rapid detection and characterization of environmental DNA signals in the field.
• Pathogen detection: Enables near real-time identification of pathogens from MinION sequencing data.
• Biodiversity studies: Supports rapid species identification and community composition analysis for biodiversity assessments.
• In-situ genomic research: Expands capacity for genomic analyses in remote or resource-limited settings due to low computational requirements.

Methodology:

Uses advanced algorithms optimized for data processing efficiency with configurable base-caller settings to trade accuracy for speed, implemented to run on a laptop CPU without GPU dependency.