Guppy

Introduction

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

For more information, please check its | Docker hub: https://hub.docker.com/r/genomicpariscentre/guppy and its home page: https://community.nanoporetech.com.

Versions

• 6.0.1

• 6.5.7

Commands

• guppy_aligner

• guppy_barcoder

• guppy_basecall_server

• guppy_basecaller

• guppy_basecaller_duplex

• guppy_basecaller_supervisor

• guppy_basecall_client

Module

You can load the modules by:

module load biocontainers
module load guppy

Example job

Warning

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