Nanocall: An Oxford Nanopore Basecaller

Installation

Nanocall can be built from source in a classical UNIX environment, or directly under Docker. The Docker build might run under Windows, though this is not tested.

Under a Classical UNIX Environment

Nanocall uses cmake for configuration and make for building. The prerequisites needed for building are zlib, hdf5, and seqan. On UNIX systems, hdf5 can be optionally built as a submodule. Look here for information on installing seqan. Example build:

mkdir /some/source/dir && cd /some/source/dir
git clone --recursive https://github.com/mateidavid/nanocall.git
cd nanocall
mkdir build && cd build
cmake ../src [-DCMAKE_INSTALL_PREFIX=/some/install/dir] [-DBUILD_HDF5=1] [-DHDF5_ROOT=/path/to/hdf5]
make
make install
/some/install/dir/bin/nanocall --version

NOTES:

• The default install prefix is /usr/local.
• Setting BUILD_HDF5 will cause hdf5 to be downloaded and built as a submodule.
• Setting HDF5_ROOT is only necessary if a copy of hdf5 is installed in a non-standard location. This is not needed when BUILD_HDF5 is used.

Under Docker

To avoid dealing with prerequisites, Nanocall can be conveniently built under Docker. Docker installation and configuration is outside of the scope of this document. Example build:

mkdir /some/source/dir && cd /some/source/dir
git clone --recursive https://github.com/mateidavid/nanocall.git
docker build -t nanocall /some/source/dir
docker run --rm nanocall

Usage Examples

# Check version
nanocall --version

# Check command line parameters
nanocall --help

# Run on single file, save output and log
nanocall /path/to/file.fast5 >output.fa 2>log

# Run on directory, using 24 threads, discard log
nanocall -t 24 /path/to/data >output.fa 2>/dev/null

# Run on file-of-file-names
nanocall /path/to/files.fofn >output.fa

# Run Docker build on directory, using 4 threads
docker run --rm -u $(id -u):$(id -g) -v /path/to/data:/data nanocall -t 4 . >output.fa

License

Released under the MIT license.