Difference between revisions of "Applications/guppy"
From HPC
m |
m (→Compute capability) |
||
| (9 intermediate revisions by the same user not shown) | |||
| Line 4: | Line 4: | ||
* Description: Local accelerated base calling for Nanopore data. | * Description: Local accelerated base calling for Nanopore data. | ||
| − | * Version: | + | * Version: 4.2.2, 6.1.7 and 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/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 is now removed from production. | |
| + | |||
| + | ==Description== | ||
| + | |||
| + | GUPPY is a program to visualize sequence annotation data of the genetic sequence data with a graphical layout. This highly interactive program allows smooth scrolling and zooming from the genomic landscape to discrete nucleic acid sequences. Its main function is the quick rendering of data on a personal computer or HPC to save the layout as a personal file. With the optional link to internet resources and printing support, this program tries to make greater use of computational media in research activity. | ||
| + | |||
==Usage Examples== | ==Usage Examples== | ||
| Line 14: | Line 20: | ||
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. | 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=== | ===Batch example=== | ||
| − | |||
| − | |||
<pre> | <pre> | ||
| Line 24: | Line 28: | ||
#SBATCH -J guppy.job | #SBATCH -J guppy.job | ||
#SBATCH --exclusive | #SBATCH --exclusive | ||
| − | #SBATCH -o | + | #SBATCH -o gpu.%j.out |
| − | #SBATCH -e | + | #SBATCH -e gpu.%j.err |
| − | #SBATCH -p | + | #SBATCH -p gpu |
| − | #SBATCH --gres=gpu | + | #SBATCH --gres=gpu |
#SBATCH --exclusive | #SBATCH --exclusive | ||
module purge | module purge | ||
module load cuda/10.1.168 | module load cuda/10.1.168 | ||
| − | module load guppy/gpu/4 | + | 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 | + | 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 |
</pre> | </pre> | ||
| Line 42: | Line 46: | ||
For applications that require this information: | For applications that require this information: | ||
| − | * | + | * NVidia A40 is 8.6 (GPU01 to GPU04) |
| − | * P100 is 6.0 | + | * NVidia P100 is 6.0 (GPU05) |
| − | |||
| − | |||
==Further Information== | ==Further Information== | ||
| Line 51: | Line 53: | ||
* https://community.nanoporetech.com/ (login required) | * https://community.nanoporetech.com/ (login required) | ||
| − | + | {{Modulepagenav}} | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Latest revision as of 12:15, 15 December 2022
Contents
Application Details
- Description: Local accelerated base calling for Nanopore data.
- Version: 4.2.2, 6.1.7 and 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.
Description
GUPPY is a program to visualize sequence annotation data of the genetic sequence data with a graphical layout. This highly interactive program allows smooth scrolling and zooming from the genomic landscape to discrete nucleic acid sequences. Its main function is the quick rendering of data on a personal computer or HPC to save the layout as a personal file. With the optional link to internet resources and printing support, this program tries to make greater use of computational media in research activity.
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 8.6 (GPU01 to GPU04)
- NVidia P100 is 6.0 (GPU05)
Further Information
- https://community.nanoporetech.com/ (login required)