Difference between revisions of "Applications/guppy"
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* Description: Local accelerated base calling for Nanopore data. | * Description: Local accelerated base calling for Nanopore data. | ||
* Version: guppy 3.1.5 to 6.4.2 | * Version: guppy 3.1.5 to 6.4.2 | ||
| − | * Modules: guppy/cpu/ | + | * Modules: guppy/cpu/4.2.2, guppy/cpu/6.1.7 and guppy/cpu/6.4.2 |
| − | * Modules: guppy/gpu/ | + | * Modules: guppy/gpu/4.2.2, guppy/gpu/6.1.7 and guppy/gpu/6.4.2 |
* Licence: Free, open-source | * Licence: Free, open-source | ||
| − | * '''Note''': guppy version 3 | + | * '''Note''': guppy version 3 is now removed from production. |
==Usage Examples== | ==Usage Examples== | ||
Revision as of 10:33, 15 December 2022
Contents
Application Details
- Description: Local accelerated base calling for Nanopore data.
- Version: guppy 3.1.5 to 6.4.2
- Modules: guppy/cpu/4.2.2, guppy/cpu/6.1.7 and guppy/cpu/6.4.2
- Modules: guppy/gpu/4.2.2, guppy/gpu/6.1.7 and guppy/gpu/6.4.2
- Licence: Free, open-source
- Note: guppy version 3 is now removed from production.
Usage Examples
Using the GPU as an accelerator 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
#!/bin/bash #SBATCH -J guppy.job #SBATCH --exclusive #SBATCH -o gpu.%j.out #SBATCH -e gpu.%j.err #SBATCH -p gpu #SBATCH --gres=gpu #SBATCH --exclusive module purge module load cuda/10.1.168 module load guppy/gpu/6.4.2 guppy_basecaller --input_path /home/user/folderIN --save_path /home/user/folderOUT --flowcell FLO-MIN106 --kit SQK-RPB004 --min_qscore 7 --qscore_filtering -x cuda:0
Compute capability
For applications that require this information:
- NVidia A40 is at least 6.0 (GPU01 to GPU04)
- NVidia P100 is 6.0 (GPU05)
Further Information
- https://community.nanoporetech.com/ (login required)