Difference between revisions of "Applications/guppy"
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==Application Details== | ==Application Details== | ||
| − | * Description: Local accelerated | + | * Description: Local accelerated base calling for Nanopore data. |
* Version: guppy 3.1.5 and 4.0.14 | * Version: guppy 3.1.5 and 4.0.14 | ||
* Modules: guppy/cpu/3.1.5 (CPU), guppy/gpu/3.1.5 (GPU), guppy/cpu/4.0.14 (CPU), guppy/gpu/4.0.14 (GPU), guppy/gpu/4.2.2 | * Modules: guppy/cpu/3.1.5 (CPU), guppy/gpu/3.1.5 (GPU), guppy/cpu/4.0.14 (CPU), guppy/gpu/4.0.14 (GPU), guppy/gpu/4.2.2 | ||
* Licence: Free, open-source | * Licence: Free, open-source | ||
| − | * '''Note''' : guppy version 3 will be removed from service soon | + | * '''Note''': guppy version 3 will be removed from service soon |
==Usage Examples== | ==Usage Examples== | ||
| − | Using the GPU as | + | 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. |
| − | Important : guppy/gpu (GPU version) requires compute level of six or above, see examples below. | + | Important: guppy/gpu (GPU version) requires to compute level of six or above, see examples below. |
===Batch example=== | ===Batch example=== | ||
Revision as of 13:35, 13 October 2022
Contents
Application Details
- Description: Local accelerated base calling for Nanopore data.
- Version: guppy 3.1.5 and 4.0.14
- Modules: guppy/cpu/3.1.5 (CPU), guppy/gpu/3.1.5 (GPU), guppy/cpu/4.0.14 (CPU), guppy/gpu/4.0.14 (GPU), guppy/gpu/4.2.2
- Licence: Free, open-source
- Note: guppy version 3 will be removed from service soon
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.
Important: guppy/gpu (GPU version) requires to compute level of six or above, see examples below.
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/4.2.2 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 cuda:1
Compute capability
For applications that require this information:
- K40m is 3.5
- P100 is 6.0
Further Information
- https://community.nanoporetech.com/ (login required)