Applications/guppy
From HPC
Contents
Application Details
- Description: Local accelerated basecalling for Nanopore data.
- Version: guppy 3.1.5
- Modules: guppy/cpu/3.1.5 and guppy/gpu/3.1.5 (GPU)
- Licence: Free, open-source
Usage Examples
Batch example
This uses 2 GPUs presently on GPU05 (compute level is high than 6) which is required by guppy's minimum requirement.
#!/bin/bash #SBATCH -J guppy.job #SBATCH --exclusive #SBATCH -o gpu05.%j.out #SBATCH -e gpu05.%j.err #SBATCH -p gpu05 #SBATCH --gres=gpu:tesla:2 #SBATCH --exclusive module purge module load cuda/10.1.168 module load guppy/gpu/3.1.5 guppy_basecaller --input_path /home/user/fast5 --save_path /home/user/guppy --flowcell FLO-MIN106 --kit SQK-RPB004 --min_qscore 7 --qscore_filtering -x cuda:0 cuda:1
Further Information
- https://community.nanoporetech.com/ (login required)