Release Notes

v2.0.2

• Migration from HMM-based BrdU detection at every thymidine to ResNet-based detection at every thymidine,
• Significant increases to BrdU detection accuracy,
• Support for BrdU detection on GPUs,
• DNAscent forkSense to call replication origins and termination sites in both synchronously and asynchronously replicating cells at any point in S-phase,
• DNAscent align to align nanopore signals to reference,
• Significant increases to replication origin calling accuracy and sensitivity,
• Visualisation utility for plotting output of multiple DNAscent executables as bedgraphs,
• Released with Boemo, MA. DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning. bioRxiv 2020.

v1.0.0

• HMM-based BrdU detection at every thymidine,
• Improvements to BrdU detection accuracy,
• DNAscent train to train Guassian mixture models from nanopolish eventalign.

v0.1.0

• HMM-based BrdU detection at ~160 thymidine-containing 6mers,
• Assignment of high- and low-BrdU regions based on Z-score,
• Replication origin calling for early S-phase cells,
• Released with Muller and Boemo, et al. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nature Methods 2019;16:429-436.