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is now deprecated and has been fully superceded byDNAscent forkSense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¶
- 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.