Nanopore Guppy¶
Dorado
Oxford Nanopore's newer Dorado is also available as a module, and delivers significantly higher performance when compared to Nanopore Guppy.
Nanopore Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
Nanopore Guppy is available as an Apptainer container on Apocrita.
Usage¶
To run the default installed version of Nanopore Guppy, simply load the
nanopore_guppy
module:
$ module load nanopore_guppy
$ nanopore_guppy guppy_basecaller --help
Usage:
With config file:
guppy_basecaller -i <input path> -s <save path> -c <config file> [options]
With flowcell and kit name:
guppy_basecaller -i <input path> -s <save path> --flowcell <flowcell name>
--kit <kit name>
List supported flowcells and kits:
guppy_basecaller --print_workflows
Use GPU for basecalling:
guppy_basecaller -i <input path> -s <save path> -c <config file>
--device <cuda device name> [options]
The above output has been truncated, run the guppy_basecaller --help
command within the container to see the full list of available options.
Example jobs¶
Serial job¶
Version >= 4.5.3 only
Only versions 4.5.3 and above work on the non-GPU nodes. If you attempt to
run an older version on a serial node, your job will fail with a missing
libcuda.so.1
error. Loading a cuda module will not solve this error.
Here is an example job running on 2 cores and 10GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=5G
module load nanopore_guppy
nanopore_guppy guppy_basecaller \
-i <input path> \
-s <save path> \
-c <config file>
GPU job¶
Here is an example job running on 8 cores and 1 GPU:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 12
#$ -l gpu=1
#$ -l h_vmem=7.5G
module load nanopore_guppy
# "--device auto" will choose GPU if available
nanopore_guppy guppy_basecaller \
-i <input path> \
-s <save path> \
-c <config file> \
--device auto