Download & Installation

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 4.0.1
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:

• pfasta (https://github.com/kloetzl/pfasta)

• fast5 (https://github.com/mateidavid/fast5.git)

• htslib (https://github.com/samtools/htslib.git)

• hdf5lib (https://support.hdfgroup.org/HDF5/)

• tinydir (https://github.com/cxong/tinydir.git)

• TensorFlow (https://www.tensorflow.org/install/lang_c)

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 on Linux.

VBZ Fast5 Compression

In new versions of MinKNOW, the 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.

GPU Use

The DNAscent detect executable can make use of a GPU, although this is optional (see detect). DNAscent requires CUDA 11.8 and cuDNN 8.9. Information about these can be found at the following links:

• cuDNN: https://developer.nvidia.com/cudnn

• CUDA: https://developer.nvidia.com/cuda-11.0-download-archive

Always discuss any installation or version changes with your system administrator.