- Bioinfo List - SeqShare Mailing Lists

[nanoporetech/dorado] Release v0.9.5 - v0.9.5
by Marco van Zwetselaar 02 Apr '25

02 Apr '25

Dear all, See below: bigger better faster, another Dorado release just out. Installation tips: scroll down to "Dorado Upgrade" in my "ONT Laptop Installation notes": https://github.com/orgs/seqafrica/discussions/2 Best wishes Marco -------- Forwarded Message -------- Subject: [nanoporetech/dorado] Release v0.9.5 - v0.9.5 Date: Mon, 31 Mar 2025 13:22:45 -0700 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) [v0.9.5](https://github.com/nanoporetech/dorado/releases/tag/v0.9.5) Repository: [nanoporetech/dorado](https://github.com/nanoporetech/dorado) · Tag: [v0.9.5](https://github.com/nanoporetech/dorado/tree/v0.9.5) · Commit: [913e1ef](https://github.com/nanoporetech/dorado/commit/913e1ef839ca27273e9d… · Released by: [iiSeymour](https://github.com/iiSeymour) [0.9.5] (31 March 2025) This release of Dorado delivers significant performance improvements and broader hardware support: - Major speed increase of the v5 SUP basecalling models on Volta (7.0) and Orin (8.7) GPUs - Enhanced speedups for HAC basecalling models on Nvidia Hopper GPUs (Compute Capability 9.0) - Support for Nvidia Blackwell GPUs (Compute Capabilities 10.0 and 12.0) Additional updates include improvements to primer sequence trimming, read orientation inference (if inferred, this will be added to the TS tag in SAM/BAM) and UMI tag sequence detection (if found, these are included in the BAM/SAM output using the RX tag). Poly(A) tail estimation accuracy has been improved, along with the stability and speed of Dorado polish and correct. Dorado aligner now supports split indexes, and the internal dependency on minimap2 has been updated to v2.28. > Note: Dorado now requires CUDA 12.8, which increases the minimum supported Nvidia driver version to 525.105. The minimum supported macOS version is now 13.0 (Ventura). For Orin platforms, JetPack 6.2 (based on Ubuntu 22.04 'Jammy Jellyfish') is now required. - [833a1aa](https://github.com/nanoporetech/dorado/commit/833a1aa98cb52b58cb83… - Improve speed of Transformer based SUP basecalling models on Volta GPUs - [d46286e](https://github.com/nanoporetech/dorado/commit/d46286e9e9f549b2f776… - Improve speed of LSTM HAC basecalling models on Hopper GPUs - [c1763b6](https://github.com/nanoporetech/dorado/commit/c1763b63001ab850d31d… - Enable Transformer SUP basecalling model performance improvements on Orin - [ee7b7cc](https://github.com/nanoporetech/dorado/commit/ee7b7ccce59eef8b5bfd… - Add caching of automatic batch size for H100 GPUs - [c946a46](https://github.com/nanoporetech/dorado/commit/c946a4657ef957c730dd… - Update minimum macOS to Ventura (version 13.0) - [99c3cb2](https://github.com/nanoporetech/dorado/commit/99c3cb2e03bfafc40e87… - Remove support for Focal and CUDA 11 on Orin - [bffa71d](https://github.com/nanoporetech/dorado/commit/bffa71d61e55b87ecb2b… - Update to JetPack 6.2 for Orin - [78260d4](https://github.com/nanoporetech/dorado/commit/78260d41aab9bd503ada… - Update to torch v2.6.0 - [0407778](https://github.com/nanoporetech/dorado/commit/04077780e9d0b9d4241c… - Update to minimap2 v2.28 - [7f4c575](https://github.com/nanoporetech/dorado/commit/7f4c57582d11e62823e6… - Add cDNA preprocessing in Dorado basecaller and trim, including UMI tag and strand orientation detection - [3232e5b](https://github.com/nanoporetech/dorado/commit/3232e5b76cd8e412f8c9… - Poly(A) tail estimation accuracy improvements - [1d384dc](https://github.com/nanoporetech/dorado/commit/1d384dc29cc0b2df2016… - Poly(A) tail estimation now consistently emits pt:i BAM tag - [56bef24](https://github.com/nanoporetech/dorado/commit/56bef2464ef5341d16db… - Ensure all valid poly(A) tails in plasmids are captured during estimation - [517d611](https://github.com/nanoporetech/dorado/commit/517d611972dba0ce8050… - Improve primer detection for kits with barcodes - [04915f3](https://github.com/nanoporetech/dorado/commit/04915f335b49f478508f… - Fix trimming of RNA reads affected by mux change and unblocking - [598d17c](https://github.com/nanoporetech/dorado/commit/598d17c6a726a307163f… - Add Dorado aligner support for split indexes - [c973914](https://github.com/nanoporetech/dorado/commit/c973914966c99f70dbaa… - Fix Dorado aligner output non-determinism - [b02d3a7](https://github.com/nanoporetech/dorado/commit/b02d3a72cfed4388b298… - Dorado polish speed improvements - [49d5aa8](https://github.com/nanoporetech/dorado/commit/49d5aa83a96ab0e89fda… - Prevent overlapping variants in Dorado polish VCF output - [e0eb79b](https://github.com/nanoporetech/dorado/commit/e0eb79b233df832b116b… - Dorado correct speed improvements in inference stage - [d520323](https://github.com/nanoporetech/dorado/commit/d520323413eecde7ce27… - Ensure Dorado does not take GPU memory on unspecified devices when using -x or --device - [48b513d](https://github.com/nanoporetech/dorado/commit/48b513daa867b2b727b7… - Fix crashes when running Dorado basecaller on systems with heterogeneous GPUs - [e8a3217](https://github.com/nanoporetech/dorado/commit/e8a3217695d907ac5ed1… - Fix inconsistency in calculation of sm/sd BAM tag values - [12ffaa3](https://github.com/nanoporetech/dorado/commit/12ffaa3eb6d255fbd0c5… - Improve error handling in model download - [4984a53](https://github.com/nanoporetech/dorado/commit/4984a530bb6a7d492321… - Dorado trim logging now reports number of reads trimmed - [8557882](https://github.com/nanoporetech/dorado/commit/85578822283197ab7e13… - Change short adapter and/or primer trimming warning to trace message - [990acb5](https://github.com/nanoporetech/dorado/commit/990acb52765734eac51b… - Add note in README for getting good performance from GPUs on Windows - [9d83b96](https://github.com/nanoporetech/dorado/commit/9d83b96d1d8f71691c8d… - Add sha256 checksums to all downloads - [4661a77](https://github.com/nanoporetech/dorado/commit/4661a77d9c6336b808d7… - Fix custom sequence format documentation - [6ed2865](https://github.com/nanoporetech/dorado/commit/6ed28652cbcaee238215… - Drop macOS/x64 pipelines — This release has 2 assets: - Source code (zip) - Source code (tar.gz) Visit the [release page](https://github.com/nanoporetech/dorado/releases/tag/v0.9.5) to download them. — You are receiving this because you are watching this repository. [View it on GitHub](https://github.com/nanoporetech/dorado/releases/tag/v0.9.5) or [unsubscribe](https://github.com/nanoporetech/dorado/unsubscribe_via_email/A… from all notifications for this repository.

1 0

Reminder: SeqAfrica April Bioinformatic CoP - Hackathon Epi2Me part 2
by Pernille Nilsson 01 Apr '25

01 Apr '25

Dear Bioinformatics Community of Practice Members, We are excited to announce our upcoming Bioinformatics Community of practice session! Ousmane Sadio will be presenting his work on hacking the Epi2Me bacterial workflow pipeline. This is a fantastic opportunity to learn more about the new capabilities of the modified workflow and the process Ousmane followed to achieve these improvements. This presentation builds on Niamh's session last month, where she discussed the SeqAfrica Senegal Hackathon. Our talented team of bioinformaticians worked to adapt an existing open-source workflow to better fit the needs of laboratories new to ONT sequencing. Please note that Denmark switched to summertime over the weekend, which may have affected the timing of the CoP. Ensure you check the time to avoid scheduling conflicts. Date: Thursday 3 April 2025 Time: 12:30 CEST Zoom link: https://dtudk.zoom.us/j/68532308758?pwd=AK8CRJQaskd7BvavJZ8RapDJ63baCg.1 Meeting ID: 685 3230 8758 Passcode: 210273 We look forward to seeing you there! Best wishes, Pernille

1 0

Reminder: SeqAfrica March Bioinformatics CoP - Hackathon on EPI2ME
by Pernille Nilsson 18 Mar '25

18 Mar '25

Dear Bioinformatics Community of Practice Members, We are excited to inform you of the upcoming Bioinformatics Community of practice session where Niamh Lacy-Roberts will present the Hackathon which took place last month in Senegal during our partners meeting. This is a great opportunity to learn more about what a hackathon is and how it was used to adapt an existing open-source workflow to better fit the needs of our laboratories new to ONT sequencing. Date: Thursday 20 March 2025 Time: 12:30 CET Zoom link: https://dtudk.zoom.us/j/68532308758?pwd=AK8CRJQaskd7BvavJZ8RapDJ63baCg.1 Meeting ID: 685 3230 8758 Passcode: 210273 Looking forward to seeing you there! Best wishes, Pernille [signature_133079383] 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>

1 0

Reminder: SeqAfrica February Bioinformatics CoP – GPT "back-end"
by Pernille Nilsson 03 Feb '25

03 Feb '25

Dear Bioinformatics Community of Practice Members, We are excited to inform you of the upcoming Bioinformatics Community of Practice session, where we will continue the topic of genomic proficiency tests. This time we will have a presentation from Lauge Holm Sørensen on the “back-end” of the DTU genomic proficiency test. This is a great opportunity to learn more about the nuts and bolts of the proficiency test and strengthen your understanding of the GPT and potentially your results (if you have participated). Date: Thursday 6 February 2025 Time: 12:30 CET Zoom link: https://dtudk.zoom.us/j/68532308758?pwd=AK8CRJQaskd7BvavJZ8RapDJ63baCg.1 Meeting ID: 685 3230 8758 Looking forward to seeing you there! Best wishes, Pernille [signature_1768105763] 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>

1 0

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

1 0

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.

1 0

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 ;-)

2 2

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>

2 1

Reminder: Bioinformatics COP tomorrow!
by Christa Twyford Gibson 04 Dec '24

04 Dec '24

Hello all, Just a gentle reminder that our bioinformatics community of practice meets tomorrow at 12:30 CET. We look forward to seeing you all there! Please see the zoom info below! Warm Regards, Christa [cid:image001.png@01DB4675.B26FA220] Christa Twyford Gibson Project Manager for SeqAfrica Project Fleming Fund Regional Grant SeqAfrica (dtu.dk)<https://www.food.dtu.dk/english/topics/antimicrobial-resistance/seqafrica> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 53 81 91 15 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/> Monthly: https://dtudk.zoom.us/meeting/u5wuceygpjwiGdEbcHdEjNfGTVqdz4TigrBi/ics?icsT… Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 --- One tap mobile +4589883788,,68365887835# Denmark +4532701206,,68365887835# Denmark --- Dial by your location • +45 89 88 37 88 Denmark • +45 32 70 12 06 Denmark • +45 32 71 31 57 Denmark • +45 32 72 80 10 Denmark • +45 32 72 80 11 Denmark • +45 47 37 25 75 Denmark Meeting ID: 683 6588 7835 Find your local number: https://dtudk.zoom.us/u/ccDieRpbcq --- Join by SIP 68365887835(a)109.105.112.236<mailto:68365887835@109.105.112.236> • 68365887835(a)109.105.112.235<mailto:68365887835@109.105.112.235> --- Join by H.323 • 109.105.112.236 • 109.105.112.235 Meeting ID: 683 6588 7835

1 0

African Bioinformatics Institute
by Marco van Zwetselaar 07 Nov '24

07 Nov '24

Dear all, Thank you all for joining today's CoP meeting, and in particular Adja for presenting the bacterial analysis pipeline developed at Institut Pasteur de Dakar! As mentioned in today's meeting, here is a link to the "African Bioinformatics Insititute" initiative: https://wellcome.org/news/were-establishing-new-institute-advance-genomics-… An in-person and virtual stakeholder meeting will take place in Cape Town on 29-30 January: https://redcap.h3abionet.org/redcap/surveys/?s=M8CWTNPP9DLC37Y9 You can express your interesting in hosting an ABI Node here: https://redcap.h3abionet.org/redcap/surveys/?s=RAA4ERLP3KNTEMKE And finally, there is an open call for the position of director here: https://tinyurl.com/yn663vm2 With thanks to @Niamh Lacy-Roberts for passing on this information Kind regards, Marco

1 0