guppy
Link to section 'Introduction' of 'guppy' Introduction
Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
Docker hub: https://hub.docker.com/r/genomicpariscentre/guppy and its home page: https://community.nanoporetech.com.
Link to section 'Versions' of 'guppy' Versions
- 6.0.1
Link to section 'Commands' of 'guppy' Commands
- guppy_aligner
- guppy_barcoder
- guppy_basecall_server
- guppy_basecaller
- guppy_basecaller_duplex
- guppy_basecaller_supervisor
- guppy_basecall_client
Link to section 'Module' of 'guppy' Module
You can load the modules by:
module load biocontainers
module load guppy
Link to section 'Example job' of 'guppy' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Guppy on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=guppy
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers guppy
guppy_basecaller --compress_fastq -i data/fast5_tiny/ \
-s basecall_tiny/ --cpu_threads_per_caller 12 \
--num_callers 1 -c dna_r9.4.1_450bps_hac.cfg