[1.3.1] (12 January 2026)

This release of Dorado updates summary files and the output structure of Dorado aligner to comply with the Oxford Nanopore Output Specifications (26.01). Changes to the file outputs include:

• Dorado summary now complies with the 26.01 Output Specifications.
• Dorado summary can now run on an input directory, and provides an optional --recursive flag.
• Dorado demux with --emit-summary now emits a full summary file, and fixes a bug causing barcode IDs to show up "unclassified" when using --emit-fastq.
• Dorado basecaller with --emit-summary now includes the correct number of samples in num_template_events in the emitted summary file.
• Dorado aligner with --emit-fastq now adds SM and al tags in emitted FASTQ files and uses these tags when populating the filepath.

This release also improves stability, including fixing a CUDA error that can arise during short read basecalling and enabling Dorado demux to run properly when the -o parameter is omitted.

• cb8fe64 - Update to specification-compliant outputs and fix several bugs for Dorado summary, demux, basecaller, and aligner
• d7a6de3 - Fix bug causing CUDA error: an illegal memory access when basecalling very short reads