Difference between revisions of "Guppy"
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Early downstream analysis components such as barcoding/demultiplexing, adapter trimming and alignment are contained within Guppy. Furthermore, Guppy now performs modified basecalling (5mC, 6mA and CpG) from the raw signal data, producing an additional FAST5 file of modified base probabilities. | Early downstream analysis components such as barcoding/demultiplexing, adapter trimming and alignment are contained within Guppy. Furthermore, Guppy now performs modified basecalling (5mC, 6mA and CpG) from the raw signal data, producing an additional FAST5 file of modified base probabilities. | ||
| + | <!--Modules--> | ||
| + | ==Environment Modules== | ||
| + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | <!--Configuration--> | ||
| + | {{#if: {{#var: conf}}|==Configuration== | ||
| + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details. | ||
| + | |}} | ||
| + | <!--Run--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
'''Warning:''' Guppy can be ''orders of magnitude'' faster when using GPUs for basecalling compared to pure CPU runs. See [[GPU Access]] for more details on how to request GPUs on HiPerGator. Here's a sample script you might want to use as a starting point: | '''Warning:''' Guppy can be ''orders of magnitude'' faster when using GPUs for basecalling compared to pure CPU runs. See [[GPU Access]] for more details on how to request GPUs on HiPerGator. Here's a sample script you might want to use as a starting point: | ||
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#SBATCH --mail-user=MYEMAIL@ufl.edu | #SBATCH --mail-user=MYEMAIL@ufl.edu | ||
#SBATCH --partition=gpu | #SBATCH --partition=gpu | ||
| − | #SBATCH --gpus=1 | + | #SBATCH --gpus=geforce:1 |
date;hostname;pwd | date;hostname;pwd | ||
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date | date | ||
</pre> | </pre> | ||
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| + | Use jobnvtop and jobhtop tools from the [[UFRC environment module]] for a real-time look at GPU and CPU processes on the job node. | ||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
Revision as of 15:05, 6 October 2020
Description
Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' basecalling algorithms, and several bioinformatic post-processing features.
Early downstream analysis components such as barcoding/demultiplexing, adapter trimming and alignment are contained within Guppy. Furthermore, Guppy now performs modified basecalling (5mC, 6mA and CpG) from the raw signal data, producing an additional FAST5 file of modified base probabilities.
Environment Modules
Run module spider guppy to find out what environment modules are available for this application.
System Variables
- HPC_GUPPY_DIR - installation directory
Additional Information
Warning: Guppy can be orders of magnitude faster when using GPUs for basecalling compared to pure CPU runs. See GPU Access for more details on how to request GPUs on HiPerGator. Here's a sample script you might want to use as a starting point:
#!/bin/bash
#SBATCH --job-name=guppy
#SBATCH --output=guppy_%j.out
#SBATCH --time=12:00:00
#SBATCH --ntasks=1
#SBATCH --mem=10GB
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=MYEMAIL@ufl.edu
#SBATCH --partition=gpu
#SBATCH --gpus=geforce:1
date;hostname;pwd
module purge
module load cuda guppy
guppy_basecaller \
--recursive \
--input_path cool_project/minion_input/fast5 \
--save_path cool_project/minion_output/basecalls \
--flowcell FLO-MIN107 --kit SQK-LSK109 \
--device "auto"
date
Use jobnvtop and jobhtop tools from the UFRC environment module for a real-time look at GPU and CPU processes on the job node.