DNAscent is software designed to detect the base analogues BrdU and EdU in single molecules of DNA sequenced on the Oxford Nanopore platform. In an experimental setup where BrdU and EdU are incorporated into nascent DNA by replication forks, this software can be used to answer questions that were traditionally answered by DNA fibre analysis. DNAscent can also be used as a replication stress assay by calling the genomic positions of fork stalls and determining the frequency of DNA breaks at replication forks.
DNAscent v4.1.1 supports sequencing data collected on Oxford Nanopore R10.4.1 flow cells. The Oxford Nanopore Flongle, MinION, GridION, and PromethION platforms are all supported.
DNAscent is under active development by the Boemo Group based in the Department of Pathology, University of Cambridge.
The recommended way to run DNAscent is via one of our supported Singularity images: https://cloud.sylabs.io/library/mboemo/dnascent/dnascent You can obtain the latest image by running:
singularity pull DNAscent.sif library://mboemo/dnascent/dnascent:4.1.1Clone the DNAscent repository with the recursive flag so that the dependencies are cloned as well.
git clone --recursive https://github.com/MBoemo/DNAscent.gitThe DNAscent directory will appear in your current directory. Switch to the latest tagged version and compile the software by running:
cd DNAscent
git checkout 4.1.1
makeThis will put the DNAscent executable into the DNAscent/bin directory. A typical compile time for DNAscent and its dependencies is 5 minutes.
Please see the documentation for detailed usage instructions, descriptions of DNAscent's subprograms, and an example workflow.
If you use DNAscent for your research, please cite the publication appropriate for the version you used:
- v3 & v4: Jones MJK, Rai SK, Pfuderer PL, Bonfim-Melo A, Pagan JK, Clarke PR, Totanes FIG, Merrick CJ, McClelland SE, Boemo MA. A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells. Nature Communications 2025. [Journal Link]
- v3: Totanes FIG, Gockel J, Chapman SE, Bartfai R, Boemo MA, Merrick CJ. A genome-wide map of DNA replication at single-molecule resolution in the malaria parasite Plasmodium falciparum. Nucleic Acids Research 2023. [Journal Link]
- v2: Boemo, MA. DNAscent v2: Detecting replication forks in nanopore sequencing data with deep learning. BMC Genomics 2021. [Journal Link]
- v1: Muller CA, Boemo MA, Spingardi P, Kessler BM, Kriaucionis S, Simpson JT, Nieduszynski CA. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nature Methods 2019. [Journal Link]
Should any bugs arise or if you have basic usage questions, please raise a GitHub issue. For more detailed discussions or collaborations, please Email Michael Boemo at mb915@cam.ac.uk.
Users wishing to analyse data acquired on legacy R9.4.1 flow cells should roll back to DNAscent v3.1.2 as v4.0.1 and above are not back-compatible with R9.4.1 flow cells. As R9.4.1 flow cells have been deprecated by Oxford Nanopore, previous versions of DNAscent designed for R9.4.1 flow cells (v3.1.2 and below) are no longer under active development.