[1.2.0] (21 October 2025)

This release of Dorado delivers major improvements to short-read (<500 bp) basecalling speed with the HAC model, bringing performance in line with that for long reads. The Dorado basecaller now more closely follows the Oxford Nanopore Output Specifications. CPU performance enhancements improve basecalling speed in cases where Dorado is not GPU-bound, such as on multi-GPU systems or when using faster models. The release also includes several other improvements and minor alignment-related bug fixes.

• a04542e - Significant improvements to short read basecalling speed
• 194b4fd - Better CPU performance in situations where Dorado is not GPU-bound
• 237dad4 - Match MinKNOW output structure from Dorado aligner or demux if output path defined
• 50c06da - Replace acquisition_start_time_ms with protocol_start_time_ms to match Oxford Nanopore Output Specification
• abe6190 - BAM tags now conform to Oxford Nanopore Output Specification
• 97c9ac3 - FASTQ files now conform to Oxford Nanopore Output Specification
• a2d0c2e - Update interpretation of alias in structured file outputs
• a9e7ced - Allow BED files with empty non-required columns to be loaded
• 74946b4 - Allow per-barcode disabling of poly(A) estimation
• 27736fc - Add support for SQK-HTB114-96 sequencing and barcoding kit
• 58ff2e3 - Move table is now emitted to FASTQ if --emit-moves is set
• 9a26d8f - Skip secondary/supplementary records from input aligned BAM in Dorado aligner
• ac36219 - Dorado basecaller will scale input data based on open_pore_level if present in POD5 files
• 9342836 - Support Dorado basecaller model discovery from --models-directory if a full model name is specified
• 86c52bd - Enable automatic batch size selection in Dorado variant and polish
• 8f7b016 - Update to Torch 2.7.1 and switch to using shared Torch libraries
• 25077dc - Update POD5 library to 0.3.34
• 08070f3 - Fix handling of BAM files with duplicate identical primary alignments in Dorado polish and variant
• ef1a032 - Fix emission of BAM tags when realigning reads in Dorado aligner
• 3357b0e - Fix crash when failing to open an output file in Dorado demux
• d2df140 - Clarify error when minimap2 fails due to memory allocation failure
• 4804278 - Improve error message in Dorado correct
• d226adb - Fix overloading of -v argument in all subcommands