Dorado is a basecaller for Oxford Nanopore reads.

• dorado on GitHub

• Module Name: dorado (see the modules page for more information)
• Requires a V100/V100x or newer GPU for basecalling. Alignment is not accelerated.
• Models are found in ${DORADO_MODELS}
• Example files in ${DORADO_TEST_DATA}

The latest dorado version with support for Fast5 files and DNA R10.4.1 4kHz data, DNA R9.4.1, and RNA002 basecalling models is v0.9.6. See the v1.0 release notes.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=gpu:v100x:1,lscratch:200 --mem=16g --cpus-per-task=6
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load dorado
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ cp -rL "${DORADO_TEST_DATA:-none}" input
[user@cn3144 ~]$ ls -lh input
-rw-r--r--. 1 user group 20G Jun  2 17:21 reads.pod5
[user@cn3144 ~]$ # emits unaligned bam by default
[user@cn3144 ~]$ dorado basecaller --device cuda:all ${DORADO_MODELS}/dna_r10.4.1_e8.2_400bps_hac@v4.3.0 ${DORADO_TEST_DATA}/r10.4.1.pod5 > output.bam
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Dorado scaling

Dorado scales well to 4 v100X GPUs. For a100 GPUs 3 or fewer GPUs are ideal. Please keep in mind that jobs allocating multiple GPUs may be queued for a longer time waiting for resources.

Create a batch input file (e.g. dorado.sh). For example:

#!/bin/bash
set -e
module load dorado
cd /lscratch/$SLURM_JOB_ID
dorado basecaller --device cuda:all ${DORADO_MODELS}/dna_r10.4.1_e8.2_400bps_hac@v4.3.0 ${DORADO_TEST_DATA}/r10.4.1.pod5 > output.bam

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=16g --gres=lscratch:50,gpu:v100x:1 --partition=gpu dorado.sh