Applications/guppy

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)

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