Difference between revisions of "Applications/guppy"

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m (Compute capability)
 
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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 and 4.0.14
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* Version: 4.2.2, 6.1.7 and 6.4.2
* 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
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* Modules: guppy/cpu/4.2.2, guppy/cpu/6.1.7 and guppy/cpu/6.4.2
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* 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 will be removed from service soon
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'''Note''': guppy version 3 is now removed from production.
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==Description==
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 +
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.
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==Usage Examples==
 
==Usage Examples==
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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.
  
Important: guppy/gpu (GPU version) requires to compute level of six or above, see examples below.
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===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.
 
  
 
<pre>
 
<pre>
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#SBATCH -J guppy.job
 
#SBATCH -J guppy.job
 
#SBATCH --exclusive
 
#SBATCH --exclusive
#SBATCH -o gpu05.%j.out
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#SBATCH -o gpu.%j.out
#SBATCH -e gpu05.%j.err
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#SBATCH -e gpu.%j.err
#SBATCH -p gpu05
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#SBATCH -p gpu
#SBATCH --gres=gpu:tesla:2
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#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/4.2.2
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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 cuda:1
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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>
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For applications that require this information:
 
For applications that require this information:
  
* K40m is 3.5
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* NVidia A40 is 8.6 (GPU01 to GPU04)
* P100 is 6.0
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* NVidia P100 is 6.0 (GPU05)
 
 
 
 
  
 
==Further Information==
 
==Further Information==

Latest revision as of 12:15, 15 December 2022

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





Modules | Main Page | Further Topics