Difference between revisions of "Guppy"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|guppy}} | |{{#vardefine:app|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. | ||
| − | '''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: | + | <!--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 Guppy GPU script you might want to use as a starting point: | ||
| + | ===GPU Job Example=== | ||
| + | <div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;"> | ||
| + | ''Expand to view GPU script sample.'' | ||
| + | <div class="mw-collapsible-content" style="padding: 5px;"> | ||
<pre> | <pre> | ||
#!/bin/bash | #!/bin/bash | ||
| Line 34: | Line 49: | ||
#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 | ||
| Line 49: | Line 64: | ||
date | date | ||
</pre> | </pre> | ||
| − | < | + | </div> |
| − | + | </div> | |
| − | + | Use jobnvtop and jobhtop tools from the [[UFRC environment module]] for a real-time look at GPU and CPU processes on the job node. | |
| − | == | + | |
| − | + | ===CPU Job Example=== | |
| − | + | If you don't have access to GPUs then set | |
| − | + | #SBATCH --ntasks=1 | |
| − | + | #SBATCH --cpus-per-task=X | |
| − | + | ||
| − | + | in the resources request section and use the corresponding guppy_basecaller arguments to set the number of basecallers and threads to use CPUs: | |
| − | + | ||
| + | --cpu_threads_per_caller X --num_callers 1 | ||
| − | + | where X is the same numbers in both sections. You can parallelize callers if appropriate. | |
|}} | |}} | ||
Latest revision as of 21:07, 14 December 2022
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 Guppy GPU script you might want to use as a starting point:
GPU Job Example
Expand to view GPU script sample.
#!/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.
CPU Job Example
If you don't have access to GPUs then set
#SBATCH --ntasks=1 #SBATCH --cpus-per-task=X
in the resources request section and use the corresponding guppy_basecaller arguments to set the number of basecallers and threads to use CPUs:
--cpu_threads_per_caller X --num_callers 1
where X is the same numbers in both sections. You can parallelize callers if appropriate.