[1.4.0] (19 February 2026)

This release of Dorado introduces new RNA v5.3.0 basecalling models, CRAM support, and a variety of other improvements and fixes.

The new RNA models address an issue causing decreased coverage at the 3' end of reads in RNA v5.2.0 models.

CRAM output is enabled using --emit-cram. Compression when using CRAM depends on the content of the output files. When basecalling with all-context modifications (5mC, 5hmC, 6mA) and --emit-moves, internal benchmarks showed ~35% smaller files with CRAM compared to BAM output.

Other changes include improvements to local haplotagging in Dorado variant, enabling GPU acceleration for Dorado correct on macOS when available, and bug fixes for Dorado demux and summary.

• 952de0b - RNA v5.3.0 basecalling models
• 1cc38b6 - Add CRAM support using --emit-cram
• 735ef54 - Updates and improvements to local haplotagging in Dorado variant
• ccc6b94 - Make the Dorado polish and variant config parameter basecaller_model optional
• ea12c45 - Dorado correct now uses GPU if available on MacOS
• cce7969 - Enable poly(A) calibration with Transformer-based models
• cbbe6dc - Fix move table output and metadata when performing sequence-based RNA trimming
• 635fc93 - Update minimap2 build to use SSE4.1 optimisations
• eb3aa6f - Add TWIST-96B-UDI, TWIST-96C-UDI, and TWIST-96D-UDI barcodes
• 28176dd - Report the number of midstrand barcodes detected in Dorado demux output summary
• 190fd11 - Fix crash in Dorado demux for BAMs without RG lines
• 081a09e - Restrict RG header lines to just the read groups that can be emitted to the target file
• 7213ebe - Fix incorrect alignment genome in Dorado summary outputs when BAM file header contains multiple unordered SQ lines