Guppy¶

Guppy is a data toolkit for Oxford Nanopore Technologies' sequencing platforms. The bundle packages version 6.5.7.

Usage example¶

If the system has a NVIDIA GPU then the following loads the Guppy bundle:

1	`module load guppy`

With the module loaded, Guppy can be run as shown below:

autoconfigure_guppy_server.py
bam_convert
crashpad_handler
guppy_aligner
guppy_barcoder
guppy_basecall_client
guppy_basecaller
guppy_basecaller_duplex
guppy_basecaller_supervisor
guppy_basecall_server minimap2

The guppy_shell can be used to access a shell in the bundle.

1	`guppy_shell`

If the system does not have NVIDIA GPU then the submit command can be used to submit a GPU job and run guppy commands.

Basecalling example:

submit --profile=vnc_gpu --name=guppy_test --gpu=2 --threads=16 --memory=128gb --input='fast5/*' --output='guppy_output/*' --module=guppy --command=guppy_basecaller -- -i fast5/ -r -s guppy_output -c dna_r9.4.1_450bps_hac.cfg -x "\"cuda:\$CUDA_VISIBLE_DEVICES\""

Barcoding example:

submit --profile=vnc_gpu --name=barcoding --gpu=2 --threads=16 --memory=128gb --hours=2 --module=guppy --command=guppy_barcoder -- -i fastq -r -s barcoding.out.dir --barcode_kits SQK-RBK004 --trim_barcodes --trim_adapters -x "\"cuda:\$CUDA_VISIBLE_DEVICES\""

Print wworkflows example:

submit --profile=vnc_gpu --name=print --gpu=1 --threads=1 --memory=8gb --hours=1 --module=guppy --command=guppy_basecaller -- --print_workflows

Adjust according to your needs.

Performance notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

Community guides and tutorials¶

No community guides available.

Official site and documentation¶

Site

Licensing information¶

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

Primary citation¶

External guides and resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za