v0.9.1

[0.9.1] (21 Jan 2025)

This release of Dorado brings significant basecalling speed improvements for Nvidia GPUs with compute capabilities 8.6 (Ampere – e.g., RTX A6000), 8.7 (Ampere – e.g., Orin family), and 8.9 (Ada Lovelace). Additionally, dorado polish receives major enhancements, including the introduction of the --bacteria flag, which optimizes basecalling for native bacterial and methylated DNA. The updated dorado polish is now compatible with data basecalled using v4.3 and v4.2 models and serves as a beta-stage replacement for Medaka.

• d46286e - Upgraded to Koi v0.5.3 for optimised basecalling on CC 8.6, 8.7 & 8.9
• 9c83c49 - Added VCF output to the Dorado polish
• d859977 - Improve messaging when an unrecognised model complex is specified
• 06f6239 - Support for legacy count models in Dorado polish
• e51d64f - Fixed precision issue with Dorado polish qscore normalisation
• d50494d - Added --bacteria support for Dorado polish
• f3fa447 - Added ULK114 kits to adapter/primer trimming LUT
• 1a4316e - Dorado polish algorithm improvements and refactoring
• a0fc960 - Dorado polish option -o now writes to a directory
• 7ae31a8 - Dorado polish fix for parsing FASTA file inputs
• b382344 - Dorado polish models are now included in Dorado download --list, --list-yaml, and --list-structured
• adebcc5 - Ensure Q-score and read length filters are applied to reads after trimming
• 96d574d - Enforce use of --kit-name for Dorado demux custom barcodes to prevent unclassified reads
• 62c86d0 - Support CUDA_VISIBLE_DEVICES for UUIDs or integers
• c39f906 - Prevent crashing in auto batchsize due to short chunksizes