guppy-software
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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
- Version: 6.0.1
- Added: July, 2021
- Updated: May, 2022
- Models: /export/apps/guppy/6.0.1/data
- Version check: https://hub.docker.com/r/genomicpariscentre/guppy-gpu/tags
Usage
See versions that are available:
$ module avail guppy
Load one version into your environment and run it:
$ module load guppy/6.0.11
Note: guppy ships with some pre-configured models that set many basecalling parameters to sensible defaults. Please consult: /export/apps/guppy/6.0.1/data.
Installation
Notes from the sysadmin during installation.
$ cd /tmp $ wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_6.0.1_linux64.tar.gz $ sudo cp -r ont-guppy /export/apps/guppy/6.0.1
Run some test data using fourteen CPUs:
$ mkdir -p /var/scratch/aorth/2022-05-24-guppy $ cd /var/scratch/aorth/2022-05-24-guppy $ wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Data_Group1.tar.gz $ tar xf Data_Group1.tar.gz $ guppy_basecaller --compress_fastq -i data/fast5_tiny/ -s data/basecall_tiny/ --cpu_threads_per_caller 14 --num_callers 1 -c dna_r9.4.1_450bps_hac.cfg ... Caller time: 3281435 ms, Samples called: 27619692, samples/s: 8416.96
Run some test data using a GPU (currently only on compute06):
$ guppy_basecaller --device "cuda:0" --compress_fastq -i data/fast5_tiny/ -s /var/scratch/aorthdata/basecall_tiny/ -c dna_r9.4.1_450bps_hac.cfg ... Caller time: 2994 ms, Samples called: 27619692, samples/s: 9.22501e+06
guppy-software.1653386354.txt.gz · Last modified: 2022/05/24 09:59 by aorth