ONT Guppy GPU

This is the landing page for ONT Guppy GPU (henceforth referred to as Guppy) which contains examples, tutorials and other contributed resources for using Guppy on the UFS HPC.

Guppy is a data toolkit for Oxford Nanopore Technologies' sequencing platforms. This version of Guppy is specifically optimized to run on GPUs.

The full suite of applications are available on the UFS HPC as a loadable module. Currently, the most commonly used application in the suite is the base caller and as such, it is best executed via a non-interactive job submission script on the UFS HPC.

UFS HPC Usage Example

The ONT Guppy GPU module can be loaded as follows (The latest version is 6.0.1):

$ module load life-sciences/ont-guppy-gpu/6.0.1

A non-interactive submission script is also currently implemented for the base caller, but can be modified to run any of the applications in the suite. The submission script template can be downloaded here.

Follow these steps to submit a Guppy job:

  1. Download the submission script

  2. Create a directory in your home directory and copy the relevant input files into this directory.

  3. Open the script in a text editor and edit the relevant variable according to the script reference

  4. Use the qsub command with the script to submit the job:

    $ qsub ont-guppy-gpu.submit

  5. Make sure the job is running (R) by using qstat To monitor the progress of the job in more detail, view the .output file created in the submission directory.

  6. When the job is complete, the output files should be present in the directory from which the submission script was submitted.

Performance Notes

  • 2 GPU
  • 16 - 32 CPU cores
  • 1 Node

  • 16 GB Memory

  • Guppy can utilize multiple GPUs, however, according to these benchmarks from the NIH Biowolf HPC cluster, scaling beyond 2 GPUs is poor. Thus it is recommended to use 2 GPUs in most cases.

Benchmarks

No benchmarks are currently available for this software on the UFS HPC.

UFS HPC Community Guides and Tutorials

  • No community guides are available.

Official site and documentation

Licensing Information

  • The binaries for Guppy is licensed under a proprietary license.
  • Only researchers who owns a Oxford Nanopore sequencing device can currently use Guppy

Primary citation

External Guides and Resources