ReadBouncer

ReadBouncer: Adaptive Sampling and Read Classification for Nanopore Sequencing

ReadBouncer enables adaptive sampling in nanopore sequencing by performing real-time rejection of non-target sequences to enrich low-abundance nucleotide sequences and deplete overrepresented sequences directly within individual nanopores.

Key Features:

• Adaptive Sampling Efficiency: Combines fast CPU and GPU base calling with read classification using Interleaved Bloom Filters to improve sensitivity and specificity, enabling enrichment of low-abundance sequences and exclusion of reads from large reference sequences, including human-sized references.
• Commodity Hardware Compatibility: Operates efficiently without mandatory GPU dependence, supporting scalable adaptive sampling on standard computational infrastructure.

Scientific Applications:

• Targeted Sequencing and Rare Variant Detection: Supports enrichment of low-abundance nucleotide sequences in metagenomics, pathogen detection, and personalized medicine to identify rare genetic variants or organisms.

Methodology:

Integrates rapid base calling with read classification via Interleaved Bloom Filters to discriminate target and non-target sequences in real time, enabling precise sequence rejection during nanopore sequencing while maintaining high throughput and classification accuracy.