Guppy (GPU)

Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' basecalling algorithms, and several bioinformatic post-processing features.

The GPU version of guppy is significantly faster than the CPU version, and should be run on a partition/node with CUDA (GPU compute) support.

The GPU-enabled guppy is made available on the cluster as a shared Apptainer container image.

You can use the apptainer/guppy module to add a convenient alias to running dorado within the container.

To use any of the aliases in a non-interactive/SLURM batch script, add the following in your script before using the alias:

Terminal

shopt -s expand_aliases

Terminal

module avail guppy
module load apptainer/guppy-gpu/6.4.6
# The following is required to use aliases in a non-interactive/SLURM batch script:
shopt -s expand_aliases
guppy_basecaller ....

Alternatively run with apptainer directly; i.e. To run binaries within the container, prefix any command with apptainer run --nv <$APPTAINER_IMG/apptainer_image.sif>. Make sure to specify --nv To enable GPU support.

Terminal

apptainer run --nv $APPTAINER_IMG/guppy-gpu.sif guppy_basecaller <guppy options>

Spack

Alternatively guppy (ont-guppy) can also be installed using Spack.