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 and 4.0.14 |
| − | * Modules: guppy/cpu/3.1.5 (CPU) | + | * 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) |
* Licence: Free, open-source | * Licence: Free, open-source | ||
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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. | 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. | ||
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| + | Important : guppy/gpu (GPU version) requires compute level of six or above, see examples below. | ||
===Batch example=== | ===Batch example=== | ||
| − | This uses 2 GPUs presently on GPU05 (compute level is high than 6) which is required by guppy's minimum requirement. | + | This uses 2 GPUs presently on GPU05 ('''compute level is high than 6''') which is required by guppy's minimum requirement. |
<pre> | <pre> | ||
Revision as of 11:22, 10 August 2020
Contents
Application Details
- Description: Local accelerated basecalling 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)
- 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.
Important : guppy/gpu (GPU version) requires 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/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
Compute capability
For applications that require this information:
- K40m is 3.5
- P100 is 6.0
Further Information
- https://community.nanoporetech.com/ (login required)