FYI, a new Dorado basecaller is out, supposedly much faster on newer GPUs, and now with flag --bacteria that uses models optimised for bacterial DNA.
ONT are also working toward integrating Medaka in Dorado, as discussed here[1], but this is currently still beta-level.
Best wishes, Marco
[1] https://github.com/nanoporetech/medaka/issues/546
-------- Forwarded Message -------- Subject: [nanoporetech/dorado] Release v0.9.1 - v0.9.1 Date: Tue, 21 Jan 2025 06:55:17 -0800 From: Chris Seymour [notifications@github.com](mailto:notifications@github.com) Reply-To: nanoporetech/dorado [noreply@github.com](mailto:noreply@github.com) To: nanoporetech/dorado [dorado@noreply.github.com](mailto:dorado@noreply.github.com) CC: Subscribed [subscribed@noreply.github.com](mailto:subscribed@noreply.github.com)
[v0.9.1](https://github.com/nanoporetech/dorado/releases/tag/v0.9.1)
Repository: [nanoporetech/dorado](https://github.com/nanoporetech/dorado) · Tag: [v0.9.1](https://github.com/nanoporetech/dorado/tree/v0.9.1) · Commit: [77b58fe](https://github.com/nanoporetech/dorado/commit/77b58fead2827517ac4bcbc9495459...) · Released by: [iiSeymour](https://github.com/iiSeymour)
[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](https://github.com/nanoporetech/dorado/commit/d46286e9e9f549b2f776f2d86e5bf0...) - Upgraded to Koi v0.5.3 for optimised basecalling on CC 8.6, 8.7 & 8.9 - 6de083d977a0f33398fb1f82e9e0df621ea5360b - Added VCF output to the Dorado polish - [d859977](https://github.com/nanoporetech/dorado/commit/d8599772fdc2e7c3374cb618cde9bf...) - Improve messaging when an unrecognised model complex is specified - [06f6239](https://github.com/nanoporetech/dorado/commit/06f62390bdd5cbbf024bff53a190b3...) - Support for legacy count models in Dorado polish - [e51d64f](https://github.com/nanoporetech/dorado/commit/e51d64fe88aa9dee99829de9cc181a...) - Fixed precision issue with Dorado polish qscore normalisation - [d50494d](https://github.com/nanoporetech/dorado/commit/d50494d16c27d3e40228b32bca0e91...) - Added --bacteria support for Dorado polish - [f3fa447](https://github.com/nanoporetech/dorado/commit/f3fa4473a6eec4224be69e538907a3...) - Added ULK114 kits to adapter/primer trimming LUT - [1a4316e](https://github.com/nanoporetech/dorado/commit/1a4316efc3d589ebfa5e0705007e40...) - Dorado polish algorithm improvements and refactoring - [a0fc960](https://github.com/nanoporetech/dorado/commit/a0fc96001862ac751b23b03842c69e...) - Dorado polish option -o now writes to a directory - [7ae31a8](https://github.com/nanoporetech/dorado/commit/7ae31a85018287fdf407e090dbad5f...) - Dorado polish fix for parsing FASTA file inputs - [b382344](https://github.com/nanoporetech/dorado/commit/b382344de58bf10ed07ed4ea6f6be1...) - Dorado polish models are now included in Dorado download --list, --list-yaml, and --list-structured - [adebcc5](https://github.com/nanoporetech/dorado/commit/adebcc5346c209888d3236ecfc9b72...) - Ensure Q-score and read length filters are applied to reads after trimming - [96d574d](https://github.com/nanoporetech/dorado/commit/96d574d9658c0096811338c9d4071a...) - Enforce use of --kit-name for Dorado demux custom barcodes to prevent unclassified reads - [62c86d0](https://github.com/nanoporetech/dorado/commit/62c86d08a4cceee470f2cd87131353...) - Support CUDA_VISIBLE_DEVICES for UUIDs or integers - [c39f906](https://github.com/nanoporetech/dorado/commit/c39f9064f200ca4cc9f2afbfc4b1e5...) - Prevent crashing in auto batchsize due to short chunksizes —
This release has 2 assets:
- Source code (zip) - Source code (tar.gz)
Visit the [release page](https://github.com/nanoporetech/dorado/releases/tag/v0.9.1) to download them.
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