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


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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>
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v0.9.1

Repository: nanoporetech/dorado · Tag: v0.9.1 · Commit: 77b58fe · Released by: 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.

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