Release Notes

v3.0.2

  • DNAscent detect now detects two different thymidine analogues, BrdU and EdU, in the same molecule,
  • DNAscent forkSense now uses the spatial patterning of EdU and BrdU to determine fork direction as in DNA fibre,
  • dnascent2bedgraph utility updated to plot both EdU and BrdU tracks in genome browsers,
  • DNAscent regions is now deprecated and has been fully superceded by DNAscent forkSense,
  • DNAscent psl is now deprecated as reads can be more comprehensively plotted using the dnascent2bedgraph utility,
  • Migration from Tensorflow 1.14 to 2.4.1 and, correspondingly, GPU usage now requires CUDA 11 and cuDNN 8,
  • Released with Totanes FIG, Gockel J, Chapman SE, Bartfai R, Boemo MA, Merrick CJ. Replication origin mapping in the malaria parasite Plasmodium falciparum. bioRxiv.

v2.0.0

  • 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,
  • 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. BMC Genomics 2021;22:430.

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