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guppy

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

See this tutorial: https://denbi-nanopore-training-course.readthedocs.io/en/latest/basecalling/basecalling.html

Information

Usage

See versions of guppy that are available:

$ module avail guppy

Load one version into your environment and run it:

$ module load guppy/5.0.11

Note: guppy ships with some pre-configured models that set many basecalling parameters to sensible defaults. Please consult: /export/apps/guppy/5.0.11/data.

Installation

Notes from the sysadmin during installation.

$ cd /tmp
$ wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_5.0.11_linux64.tar.gz
$ tar xf ont-guppy_5.0.11_linux64.tar.gz
$ sudo mkdir -p /export/apps/guppy
$ sudo cp -r ont-guppy /export/apps/guppy/5.0.11

Run some test data using fourteen CPUs:

$ cd /var/scratch
$ mkdir -p /var/scratch/aorth/2021-07-01-guppy
$ wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Data_Group1.tar.gz
$ tar xf Data_Group1.tar.gz -C /var/scratch/aorth/2021-07-01-guppy
$ guppy_basecaller --compress_fastq -i /var/scratch/aorth/2021-07-01-guppy/data/fast5_tiny/ -s /var/scratch/aorth/2021-07-01-guppy/data/basecall_tiny/ --cpu_threads_per_caller 14 --num_callers 1 -c dna_r9.4.1_450bps_hac.cfg
...
Caller time: 208271 ms, Samples called: 27619692, samples/s: 132614

Run some test data using a GPU (currently only on compute06):

$ guppy_basecaller --device "cuda:0" --compress_fastq -i /var/scratch/aorth/2021-07-01-guppy/data/fast5_tiny/ -s /var/scratch/aorth/2021-07-01-guppy/data/basecall_tiny/ -c dna_r9.4.1_450bps_hac.cfg
...
Caller time: 2994 ms, Samples called: 27619692, samples/s: 9.22501e+06
guppy-software.txt · Last modified: 2021/07/08 08:11 by aorth