Software for detecting contiguous regions of base analogues incorporated in Oxford Nanopore reads. Development was done using gcc 5.4.0 on an Ubuntu 16.04 platform.
The recommended OS for DNAscent is Ubuntu 16.04. Clone 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 3.1.2
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.
Please cite our publications if you use DNAscent for your research:
- Jones MJK, Rai SK, Pfuderer PL, Bonfim-Melo A, Pagan JK, Clarke PR, McClelland SE, Boemo MA. A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells. bioRxiv. [bioRxiv]
- Totanes FIG, Gockel J, Chapman SE, Bartfai R, Boemo MA, Merrick CJ. Replication origin mapping in the malaria parasite Plasmodium falciparum. bioRxiv. [bioRxiv]
- Boemo, MA. DNAscent v2: Detecting replication forks in nanopore sequencing data with deep learning. BMC Genomics 2021;22:430. [Journal Link]
- 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;16:429-436. [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.