v2.1.1

[2.1.1] (30 July 2026)

This version of Dorado includes bug fixes following the Dorado 2.1.0 release.

• 5174cb76ae721954b96c62cb8f94bff2120c7492 - Fix minor non-determinism when running v5.0.0 onwards SUP models with variable chunk size optimisation.
• 73bd3182fa728ad2c49b41bb04d3de715f20e279 - Fix occurrence of variants with missing alt alleles and incorrect genotype in Dorado smallvar.

v1.3.3

[1.3.3] (22 July 2026)

This release of Dorado adds support for PromethION Plus (FLO-PRO114P) Flow Cells. Note that this support is not yet included in later releases. This release also contains bug fix backports. Dorado 1.3.3 is the version included in the MinKNOW 26.01 Long Term Support (LTS) release.

• 7733775 - Update OpenSSL to 3.5.7.
• 7213ebe - Fix incorrect alignment genome in Dorado summary outputs when BAM file header contains multiple unordered SQ lines.
• 3ad7bdd - Fix crash when running Dorado demux on input BAM files without RG lines.
• 5edc343 - Add Fast, HAC and 5mCG/5hmCG models for FLO-PRO114P flowcells.

v2.1.0

[2.1.0] (13 July 2026)

This version of Dorado introduces performance improvements for v6.0.0 HAC models on Blackwell GPUs. Performance of v5.0.0+ SUP models has also been improved, especially for short reads. This release also contains a collection of feature improvements and bug fixes for Dorado smallvar, including initial gVCF support.

• 9829da3 - Update to Koi 0.7.3 with improved Blackwell performance for v6.0.0 HAC models.
• 0917d62 - Add support for variable chunk size basecalling for v5.0.0 onwards SUP models, improving performance for short reads.
• b779ea1 - Improve the CPU efficiency of read splitting.
• 4fa5164 - Support gVCF output from Dorado smallvar via the --gvcf option.
• 1946d7a - Correctly report variants in Dorado smallvar when the reference is lower case.
• c5a3cde - Sort and deduplicate processed_regions.bed file in Dorado smallvar.
• 44442d1 - Add --hemizygous-regions option to Dorado smallvar, to specify regions in which haploid variant calls are expected.
• 9f11663 - Remove duplicated fileformat header line from VCF output.
• bd56aac - Bug fix for overlapping simple variants by removing redundant allele coverage check in Dorado smallvar.
• b72ad62 - Fix output of overlapping variants due to trimming of processed regions before merging.
• 36e332a - Add --MD, --cs and --rmq to the list of supported minimap options.
• 7f72ddc - No longer create a .fai index file on disk alongside alignment references.
• ab8217e - Fix sp:i tag to contain the correct split points in all cases when a read has been split multiple times.
• ae09deb - Add support for single-ended dual barcode arrangements (two barcodes at one end of a read) and arrangements with split inter-barcode flanking regions.
• 9ba24c5 - Port the Dorado correct Herro model from TorchScript to Libtorch.
• 765ea19 - Remove use of TorchScript from Dorado.
• 7cbf1c3 - Update to minimap2 v2.31.
• 8678916 - Pin POD5 version to 0.3.39.
• 7d36a47 - Fix batch size benchmarking while running LSTM models with variable chunk sizes.

v2.0.1

[2.0.1] (15 June 2026)

This version of Dorado introduces fixes and enhancements following the Dorado 2.0.0 release. Improvements include adding a @PG ID:aligner header line from Dorado basecaller, allowing Dorado smallvar to consume reads aligned inline with basecaller; preventing unnecessary poly(A) worker threads and improving poly(A) thread count determination; initial Apple Silicon implementation for v6.0.0 HAC on MacOS; pre-computed batch size benchmarks for a wider variety of GPUs; and several other fixes improving compatibility with v6.0.0 models.

• 2ab1fc1 - Dorado basecaller command now adds a @PG ID:aligner header line
• 242635d - Fix "bad any_cast" error when using modified-bases-threshold argument
• fcacebe - Fix Dorado duplex command when running DNA HAC v6.0.0 model
• c759689 - Fix MD5 sums for M5 tags to conform to the SAM spec
• cc2eed2 - Only create poly(A) worker threads when poly(A) estimation is enabled
• fa50e60 - Add initial MPS backend implementation for v6.0.0 HAC on MacOS
• 44e9a59 - Add pre-computed batch size benchmarks for Quadro GV100
• 728b1a7 - Add pre-computed batch size benchmarks for RTX PRO 6000 variants, H100 PCIe, RTX A6000, RTX 5070 Ti and RTX 5090.
• d1725d9 - Fix a crash when running v6.0.0 HAC models on Win/Linux hosts that do not have NVIDIA drivers installed, when using CPU mode.

v2.0.0

[2.0.0] (20 May 2026)

This major release of Dorado includes new v6.0 basecalling models for DNA and RNA, state-of-the-art small variant calling capabilities with Dorado smallvar (formerly Dorado variant), and a range of other performance, usability, and stability improvements. This release introduces:

• New v6.0 basecalling models
  • A more accurate basecalling model (HAC v6.0) for DNA
    • High single-molecule accuracy with improvements in short tandem repeat expansions, homopolymers, and low-complexity regions
    • Improved accuracy in bacterial methylation motifs, enabling polished assemblies comparable to SUP v5.2
    • Updated modified base models for 5mC/5hmC, 4mC/5mC, and 6mA, with substantial improvements in modified base accuracy
  • Updated fast, HAC, and SUP models for RNA basecalling
    • Improved headline single-molecule accuracy, particularly for HAC basecalling
    • Updated models for RNA modifications, including substantial gains for HAC pseU, HAC m6A/inosine, and SUP m5C/2OmeC
  • Updated models for Dorado polish
    • New polishing model for v6.0 HAC added
    • Bacterial polishing model now also supports v6.0 HAC input data
• New Dorado smallvar tool replacing Dorado variant for SNP and INDEL calling
  • Dorado smallvar provides state-of-the-art variant calling accuracy from data basecalled with DNA HAC v6.0 and HAC v5.2 models
  • Dorado smallvar is significantly faster than Dorado variant through a novel model architecture, highly optimised GPU execution, and scalability across multiple GPU devices

Other fixes and improvements have been implemented in Dorado aligner, demux, summary, and more, with the full list of changes below.

• eba46ab - Add v6.0 DNA and RNA basecalling, modified base, and Dorado polish models, including new HAC basecall model architecture
• 0d519ea - Replace Dorado variant with Dorado smallvar
• 23e04b8 - Dorado smallvar support for v6.0 and v5.2 HAC models
• aa90f44 - Replace --model with --models-directory and --model-override in Dorado smallvar
• cb41979 - Add a --model-override option to Dorado polish
• 0f5e090 - Dorado polish now processes only the draft sequences from the input BAM file header
• f309055 - Enable the -eqx minimap2 option in Dorado aligner
• ad3f074 - Prevent excessive memory usage when running alignment
• eb1efa8 - Prevent over-splitting of RNA reads
• 49e9f07 - Improve speed of Dorado summary
• 2ed0f11 - Fix summary file output to better match results from Dorado basecall server and SAM specification
• 0fce0e0 - Initial support for custom barcoding arrangements with dual barcodes
• ae2a8b6 - Improve handling of inconsistent read group data in Dorado demux and aligner
• 0edb926 - Remove support for consuming stdin for Dorado demux
• 23f944a - Fix Dorado demux crash when running on previously demultiplexed files
• ef3835f - Fix Dorado demux crash when processing previously unclassified read groups with --no-trim flag
• d68d51d - Include tm:Z tag in output file RG lines to indicate trim conditions
• b47e64d - Prevent Dorado basecaller crash when no sample_id in POD5 file
• 757b250 - Fix output folder paths to include experiment ID when processing POD5s that were converted from .fast5
• f3758e1 - Increase minimum supported CUDA version to 12.8 (or 12.6 on Linux ARM)
• 4a4ca7a - Update to OpenSSL 3.5.5
• 9bb7296 - Update to pod5 0.3.39
• 4e39b86 - Dorado correct now defaults to CPU mode on macOS but allows a user-specified --device metal
• ceb4ba8 - Add pre-computed batch size benchmarks for RTX PRO 6000 Workstation cards

v1.4.0

[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

v1.3.2

[1.3.2] (17 February 2026)

This release of Dorado introduces a minor bugfix to Dorado demux.

• 64967d8 Fix crash when Dorado demux is provided read records with a blank "sample_id".

v1.3.1

[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

v1.3.0

[1.3.0] (21 November 2025)

This release of Dorado expands GPU compatibility with support for Nvidia DGX Spark* and Jetson Thor, and updates to Torch 2.9.0. Dorado 1.3.0 introduces an --emit-summary option in the basecaller and improved handling of modified base models, as well as several fixes to summary, demux, and basecaller and performance improvements to polish and variant.

*Please note that in this release, Dorado correct is not yet compatible with DGX Spark. This will be addressed in a future release.

• 2f55740 - Add support for DGX Spark and Jetson Thor
• bc4b95c - Update Torch to 2.9.0 for CUDA 12 onwards
• a65f9df - Add --emit-summary option to Dorado basecaller
• 47ccd2e - Enable --modified-bases-models to use modified base model names in addition to paths; clean up .temp model directories
• c91a872 - Fix bug where Dorado demux with --no-classify fails to generate separate barcode files
• 9275896 - Regenerate RG headers when running Dorado demux and fix PG header generation
• a9d7d20 - Reinstate masking of modified base probabilities which fall below a minimum threshold of 5%
• 13d4722 - Ensure Dorado summary correctly calculates number of substitutions in the absence of an MD tag
• 46be4fb - Validate the input to Dorado summary and allow streaming input to match other commands
• a52c1a0 - Fix bug causing --chunksize in Dorado basecaller to be set incorrectly when --chunksize=10000 is passed at command line
• 0c9f832 - Encoding parallelisation improvement for Dorado polish and variant from pull request #1504
• be473b1 - Refactor local haplotagging in Dorado variant
• 816bae6 - Add RTX PRO 6000 Blackwell auto batch size benchmarks
• 261a5b9 - Remove duplicated material from README.md and link to Dorado Documentation

v1.2.0

[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