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Dorado

Dorado is an easy-to-use basecaller for Oxford Nanopore reads. The bundle packages version 1.1.0.

Usage example

The following loads the Dorado bundle:

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module load dorado

The module makes the dorado and pod5 commands available. The dorado_shell command can be used to access a shell in the bundle.

Run pet list -t dorado for a list of examples.

Some Dorado subcommands write the output to stdout, for example: basecaller outputs BAM data to stdout. This is problematic when the command is run using ern jobs submit command because the redirect should be done when the job runs, not when the job is submitted. Use a wrapper script such as the one below, to correctly redirect the data to a file. An example of submitting a wrapper script is included ern jobs help.

An example script to run Dorado:

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#!/bin/bash
dorado basecaller dna_r10.4.1_e8.2_400bps_sup@v4.3.0 pod5/ \
        --min-qscore 10 --kit-name SQK-NBD114-24 \
        -x "cuda:$CUDA_VISIBLE_DEVICES" > calls.bam

dorado demux --output-dir demux/ --no-classify calls.bam

Adjust according to your needs.

Performance notes

No performance notes available

Dorado should be run on a system with at least 128 GB of RAM, 8 threads, and a NVIDIA GPU.

Benchmarks

No benchmarks available.

Community guides and tutorials

  • No community guides available.

Official site and documentation

Licensing information

Primary citation

External guides and resources

  • If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za