DNAscent

DNAscent detects BrdU base analogues in Oxford Nanopore Technologies (ONT) sequencing reads to map DNA replication dynamics at single-molecule, single-base resolution.

Key Features:

• Base analogue detection: Detects the thymidine analogue BrdU within ONT sequencing reads.
• Residual neural network: Uses a residual neural network for fast, high-precision identification of BrdU at single-base resolution.
• Autoencoder-based replication feature detection: Employs an autoencoder to detect replication forks, origins, and termination sites.
• Single-molecule and single-base resolution: Reports replication-related signals at the level of individual DNA molecules and individual bases.
• High-throughput analysis: Processes large ONT datasets to enable measurement of replication features across many reads.
• Compatibility with experimental designs: Applicable to both synchronous and asynchronous cell population experiments.
• Protocol robustness: Demonstrates robustness across various experimental protocols for BrdU incorporation and ONT sequencing.

Scientific Applications:

• DNA replication dynamics: Mapping replication fork movement and timing to study replication dynamics genome-wide.
• Origin and termination site mapping: Identifying replication origins and termination sites from single-molecule ONT data.
• Base analogue incorporation analysis: Quantifying and localizing BrdU incorporation patterns in synchronous and asynchronous cell populations.

Methodology:

DNAscent applies deep learning to ONT sequencing reads, using a residual neural network to detect BrdU and an autoencoder to identify replication forks, origins, and termination sites.