Difference between revisions of "Applications/guppy"
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* Description: Local accelerated basecalling for Nanopore data. | * Description: Local accelerated basecalling for Nanopore data. | ||
* Version: guppy 3.1.5 | * Version: guppy 3.1.5 | ||
| − | * Modules: guppy/cpu/3.1.5 and guppy/gpu/3.1.5 ( | + | * Modules: guppy/cpu/3.1.5 (CPU) and guppy/gpu/3.1.5 (GPU) |
* Licence: Free, open-source | * Licence: Free, open-source | ||
Revision as of 14:20, 14 June 2019
Contents
Application Details
- Description: Local accelerated basecalling for Nanopore data.
- Version: guppy 3.1.5
- Modules: guppy/cpu/3.1.5 (CPU) and guppy/gpu/3.1.5 (GPU)
- Licence: Free, open-source
Usage Examples
Using the GPU as accelerators will make the analysis considerably faster (on large data sets). For small runs the CPU version is recommended and probably faster by removing the GPU overhead.
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)