DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning [article]

Michael A Boemo
2020 bioRxiv   pre-print
The detection of base analogues in Oxford Nanopore Technologies (ONT) sequencing reads has become a promising new method for the high-throughput measurement of DNA replication dynamics with single-molecule resolution. This paper introduces DNAscent v2, software that uses a residual neural network to achieve fast, accurate detection of the thymidine analogue BrdU with single-base resolution. DNAscent v2 comes equipped with an autoencoder that detects replication forks, origins, and termination
more » ... tes in ONT sequencing reads from both synchronous and asynchronous cell populations, outcompeting previous versions and other tools across different experimental protocols. DNAscent v2 is open-source and available at https://github.com/MBoemo/DNAscent.
doi:10.1101/2020.11.04.368225 fatcat:4i7b5zawhzfcnk4f4vtli7jhce