January 2025 - Bioinfo List - SeqShare Mailing Lists

ONT variant callers benchmark paper
by Marco van Zwetselaar 22 Jan '25

22 Jan '25

Dear all, Another shot at Illumina as the Gold Standard, now for variant calling: Hall MB, Wick RR, Judd LM, Nguyen AN, Steinig EJ, Xie O, et al. Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data. In: eLife [Internet]. eLife Sciences Publications Limited; 10 Oct 2024 [cited 22 Jan 2025]. doi:10.7554/eLife.98300 https://elifesciences.org/articles/98300 From the abstract: "We also investigated the impact of read depth on variant calling, demonstrating that 10× depth of ONT super-accuracy data can achieve precision and recall comparable to, or better than, full-depth Illumina sequencing. These results underscore the potential of ONT sequencing, combined with advanced variant calling algorithms, to replace traditional short-read sequencing methods in bacterial genomics, particularly in resource-limited settings." The authors attribute the higher recall scores of ONT variant calls (counter-intuitive given their lower average base Q-score, even if the gap with Illumina is closing) to better resolution in variant-dense and repeat regions. Cheers Marco

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Fwd: [nanoporetech/dorado] Release v0.9.1 - v0.9.1
by Marco van Zwetselaar 21 Jan '25

21 Jan '25

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(a)github.com>](mailto:notifications@github.com) Reply-To: nanoporetech/dorado [<noreply(a)github.com>](mailto:noreply@github.com) To: nanoporetech/dorado [<dorado(a)noreply.github.com>](mailto:dorado@noreply.github.com) CC: Subscribed [<subscribed(a)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/77b58fead2827517ac4b… · 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/d46286e9e9f549b2f776… - 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/d8599772fdc2e7c3374c… - Improve messaging when an unrecognised model complex is specified - [06f6239](https://github.com/nanoporetech/dorado/commit/06f62390bdd5cbbf024b… - Support for legacy count models in Dorado polish - [e51d64f](https://github.com/nanoporetech/dorado/commit/e51d64fe88aa9dee9982… - Fixed precision issue with Dorado polish qscore normalisation - [d50494d](https://github.com/nanoporetech/dorado/commit/d50494d16c27d3e40228… - Added --bacteria support for Dorado polish - [f3fa447](https://github.com/nanoporetech/dorado/commit/f3fa4473a6eec4224be6… - Added ULK114 kits to adapter/primer trimming LUT - [1a4316e](https://github.com/nanoporetech/dorado/commit/1a4316efc3d589ebfa5e… - Dorado polish algorithm improvements and refactoring - [a0fc960](https://github.com/nanoporetech/dorado/commit/a0fc96001862ac751b23… - Dorado polish option -o now writes to a directory - [7ae31a8](https://github.com/nanoporetech/dorado/commit/7ae31a85018287fdf407… - Dorado polish fix for parsing FASTA file inputs - [b382344](https://github.com/nanoporetech/dorado/commit/b382344de58bf10ed07e… - Dorado polish models are now included in Dorado download --list, --list-yaml, and --list-structured - [adebcc5](https://github.com/nanoporetech/dorado/commit/adebcc5346c209888d32… - Ensure Q-score and read length filters are applied to reads after trimming - [96d574d](https://github.com/nanoporetech/dorado/commit/96d574d9658c00968113… - Enforce use of --kit-name for Dorado demux custom barcodes to prevent unclassified reads - [62c86d0](https://github.com/nanoporetech/dorado/commit/62c86d08a4cceee470f2… - Support CUDA_VISIBLE_DEVICES for UUIDs or integers - [c39f906](https://github.com/nanoporetech/dorado/commit/c39f9064f200ca4cc9f2… - 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. — You are receiving this because you are watching this repository. [View it on GitHub](https://github.com/nanoporetech/dorado/releases/tag/v0.9.1) or [unsubscribe](https://github.com/nanoporetech/dorado/unsubscribe_via_email/A… from all notifications for this repository.

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BenchAMRking: [...] illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows
by Marco van Zwetselaar 16 Jan '25

16 Jan '25

Dear all, Oh no, not another tool with an AMRwkward name! Wasn't hAMRonization enough already? (Try typing it if you disagree.) But anyway, this looks like a valuable initiative: Strepis N, Dollee D, Vrins D, Vanneste K, Bogaerts B, Carrillo C, et al. BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows. BMC Genomics. 2025;26: 27. doi:10.1186/s12864-024-11158-5. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-11158-5 I was a bit underwhelmed by the four currently included workflows (see: https://erasmusmc-bioinformatics.github.io/benchAMRking/) of which two are Salmonella-only, one Ecoli-only, and one multi-species (abritAMR), but things can grow from here. How does it relate to hARMonization_workflow, which incorporates 18 AMR tools? BenchAMRking aims at validating AMR workflows for clinical and public health use, against a "gold standard" reference. hAMRonization_workflow was set up primarily to have a testing ground for hAMRonization, the tool to convert output from any AMR tool into a common format. As its maintainer (Finlay Maguire) said, the workflow is almost too brittle to maintain. But how else will you test hAMRonization, manually run 18 tools over a dozen inputs?! I recently submitted a bunch of patches to bring hAMRonization up to date with the latest tool versions. I also managed to upgrade hAMRonization_workflow to use all the latest tool versions. Give it a try if you're up for it: https://github.com/pha4ge/hAMRonization_workflow. It installs with a simple "conda env create". Prepare for a long wait on the first run, while it installs all tools and databases. Subsequent runs are quick: it takes ~10mn on my laptop to run all 18 tools on an isolate. Best wishes, AMRco ;-)

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Reminder: SeqAfrica January Bioinformatics CoP – Results from the genomic proficiency tests 2020-2022
by Pernille Nilsson 08 Jan '25

08 Jan '25

Dear Bioinformatics Community of Practice Members, Happy New Year and wishes for a fantastic 2025! We are excited to inform you of this year’s first Bioinformatics Community of Practice session tomorrow, where Niamh Lacy-Roberts will present the results from her draft paper titled “Whole Genome Sequencing Proficiency in African Laboratories for Antimicrobial Resistance Surveillance: Results of the SeqAfrica 2020-2022 Genomic Proficiency Tests”. Niamh would also welcome your feedback on the plots, results, and conclusions. This is a great opportunity to learn more about the progress of the genomic proficiency testing conducted in SeqAfrica and we are excited for your input! Best wishes, Pernille [signature_693501174] Dr Pernille Nilsson Pronouns: she, her Project Manager SeqAfrica National Food Institute Research Group for Global Capacity Building Mob. +45 93 51 16 54 pnil(a)food.dtu.dk<mailto:pnil@food.dtu.dk> Henrik Dams Allé Building 204 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk>

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