Guppy,  is a data processing toolkit that contains Oxford Nanopore’s (https://nanoporetech.com/) basecalling algorithms, and several bioinformatic post-processing features, such as barcoding/demultiplexing, adapter trimming, and alignment. The Guppy toolkit also performs modified basecalling (5mC, 6mA and CpG) from the raw signal data, producing an additional FAST5 file of modified base probabilities.

License and Disclaimer

“Base Caller Software” shall mean Oxford’s proprietary software, including all functional specifications associated therewith made available to the Oxford Group’s customers on the Oxford Group’s websites, as amended from time to time (the “Base Caller Documentation”), designed to convert certain Instrument
Data to Biological Data, as may be made available to Customers by Oxford, whether free of charge or for a fee.

Guppy is available to ONT customers via their community website https://community.nanoporetech.com/

Example Slurm script

  • Following Slurm script is a template to run Basecalling on NVIDIA P100 GPUs.( We do not recommend running Guppy jobs on CPUs )
  • --device auto will automatically pick up the GPU over CPU
  • Also,  NeSI Mahuika cluster can provide A100 GPUs on request which can be 5-6 times faster than P100 GPUs for Guppy Basecalling with  version. 5 and above.
    • If you wish to use the A100 GPUs please contact our support team to learn more about getting access to the A100 GPU cards.
  • Config files are stored in /opt/nesi/CS400_centos7_bdw/ont-guppy-gpu/(version)/data/  with read permissions to all researchers (replace (version) with the version of the module)


#!/bin/bash -e

#SBATCH --account nesi12345
#SBATCH --job-name ont-guppy-gpu_job
#SBATCH --gpus-per-node P100:1
#SBATCH --mem 6G
#SBATCH --cpus-per-task 4
#SBATCH --time 10:00:00
#SBATCH --output slurmout.%j.out

module purge
module load ont-guppy-gpu/6.2.1

guppy_basecaller -i /path/to/input/data/directory -s /path/to/save/fastq/files \
--config /opt/nesi/CS400_centos7_bdw/ont-guppy-gpu/6.1.2/data/nameof.cfg \
--device auto --recursive --records_per_fastq 4000 \
--calib_detect --calib_reference lambda_3.6kb.fasta --detect_mid_strand_adapter
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