Getting Started

Singularity

We recommend running DNAscent using one of our supported Singularity images. These images contain all necessary dependencies including TensorFlow, CUDA, CuDNN, and compression plugins so that your system only needs a valid NVIDIA driver for GPU usage. If your system does not have Singularity installed, instructions are available here.

singularity pull DNAscent.sif library://mboemo/dnascent/dnascent:4.2.1

You can run DNAscent from the image by passing the desired executable and arguments. The following example shows how to run DNAscent detect:

singularity run --nv DNAscent.sif detect -b /path/to/alignment.bam -r /path/to/reference.fasta -i /path/to/index.dnascent -o /path/to/output.bam

Building from Source

Clone the DNAscent repository with the recursive flag so that the dependencies are cloned as well.

git clone --recursive https://github.com/MBoemo/DNAscent.git

The DNAscent directory will appear in your current directory. Switch to the latest release and compile the software by running:

cd DNAscent
git checkout 4.2.1
make

This will put the DNAscent executable into the DNAscent/bin directory. Compilation requires a version of gcc that supports C++14, and a typical compile time for DNAscent and all of its dependencies is 5-7 minutes.

Cloning the repository recursively (see above) will provide all the required dependencies so you don’t need to find them yourself. For completeness, however, they are listed here:

Please note that the high throughput sequencing library (htslib) requires bzlib and lzma for compression. While these are common on most systems, if you don’t have these, apt-get lzma-dev, liblzma-dev, and libbz2-dev. In addition, pfasta requires libbsd.

FAST5 files are compressed with VBZ Compression (see https://github.com/nanoporetech/vbz_compression). To use DNAscent on these compressed FAST5 files, do the following (N.B., we’re assuming you don’t have root permissions):

  1. Go to https://github.com/nanoporetech/vbz_compression/releases and download the plugin appropriate for your processor architecture. In this example, we’ll use ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz.

  2. Download and unpack the plugin:

    wget https://github.com/nanoporetech/vbz_compression/releases/download/v1.0.1/ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
tar -xf ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz

  3. Add the plugin to your path:

    export HDF5_PLUGIN_PATH=/full/path/to/ont-vbz-hdf-plugin-1.0.1-Linux/usr/local/hdf5/lib/plugin

  4. Run DNAscent detect as normal.

The DNAscent detect executable can make use of a GPU, although this is optional (see detect). DNAscent requires CUDA 11.1 and cuDNN 8.0. Information about these can be found at the following links: