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Reminder: SeqAfrica Bioinformatics CoP June
by Pernille Nilsson 24 Jun '25

24 Jun '25

Dear Bioinformatics Community of Practise Members, This is a gentle reminder that we have our June session coming up on Thursday! Sade Magabotha will be presenting her script which looks for SNPs in Vibrio cholerae datasets. The github page is here https://github.com/Shaedeycool/Vibrio_SNPs. The script is set to look for SNPs with 90% similarity to the sequences in the database covering 90% of the entire length of the sequences of interest for biotype and serotype. Join us to learn more about this script! Date: Thursday 26 June 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 [http://www.dtu.dk/-/media/DTU_Generelt/Andet/mail-signature-logo.png] Dr Pernille Nilsson Project Manager SeqAfrica Pronouns: she, her Mob. +45 22 13 75 50 pnil(a)food.dtu.dk<mailto:pnil@food.dtu.dk> National Food Institute Research Group for Global Capacity Building Henrik Dams Allé Building 204 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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New date: SeqAfrica June Bioinformatic CoP - Presentation of SNP script for Vibrio cholera
by Pernille Nilsson 27 May '25

27 May '25

Dear Bioinformatics Community of Practice Members, We are happy to announce our upcoming Bioinformatics Community of practice session! This event promises to be an enlightening experience, featuring a presentation by Sade Magabotha on her script which looks for SNPs in Vibrio cholera datasets. If you are interested in exploring the details of the script in advance of the meeting, you can find the github page here: https://github.com/Shaedeycool/Vibrio_SNPs Please note the change in date from June 5th to June 26th! Date: Thursday 26 June 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 [http://www.dtu.dk/-/media/DTU_Generelt/Andet/mail-signature-logo.png] Dr Pernille Nilsson Project Manager SeqAfrica Pronouns: she, her Mob. +45 22 13 75 50 pnil(a)food.dtu.dk<mailto:pnil@food.dtu.dk> National Food Institute Research Group for Global Capacity Building Henrik Dams Allé Building 204 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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Reminder: metadata expert elicitation tomorrow
by Christa Twyford Gibson 19 May '25

19 May '25

Dear Colleagues, This is a gentle reminder that our metadata expert elicitation will take place tomorrow at 14:15 CEST. The Zoom link to join is below. We look forward to seeing you tomorrow! Kind regards, Christa ────────── Christa Twyford Gibson is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://dtudk.zoom.us/j/67066262671?pwd=yqMv6duCXRDaSZz6ytH7hVxcV8G3U0.1 Meeting ID: 670 6626 2671 Passcode: 432088 --- One tap mobile +4589883788,,67066262671#,,,,*432088# Denmark +4532701206,,67066262671#,,,,*432088# 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: 670 6626 2671 Passcode: 432088 Find your local number: https://dtudk.zoom.us/u/cdW8yWGZ3y --- Join by SIP 67066262671(a)109.105.112.236<mailto:67066262671@109.105.112.236> • 67066262671(a)109.105.112.235<mailto:67066262671@109.105.112.235> --- Join by H.323 • 109.105.112.236 • 109.105.112.235 Meeting ID: 670 6626 2671 Passcode: 432088 ────────── [cid:image001.png@01DBC8A2.9A799CC0] 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/>

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New date: SeqAfrica May Bioinformatics CoP - Outbreak Response using Genomics
by Pernille Nilsson 12 May '25

12 May '25

Dear Bioinformatics Community of Practice Members, We are thrilled to announce our upcoming Bioinformatics Community of practice session! This event promises to be an enlightening experience, featuring a presentation by Raissa MUVUNYI on "Outbreak Response Using Genomics: The case of the Marburg Outbreak in Rwanda". This session is a fantastic opportunity to delve into the transformative power of genomics in outbreak detection and response, as demonstrated by real-world efforts on the ground. Please note the change in date from May 1st to May 15th! Date: Thursday 15 May 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 [http://www.dtu.dk/-/media/DTU_Generelt/Andet/mail-signature-logo.png] Dr Pernille Nilsson Project Manager SeqAfrica Pronouns: she, her Mob. +45 22 13 75 50 pnil(a)food.dtu.dk<mailto:pnil@food.dtu.dk> National Food Institute Research Group for Global Capacity Building Henrik Dams Allé Building 204 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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You are invited to an expert elicitation on metadata for LMICs 20 May at 14:15 CET
by Christa Twyford Gibson 24 Apr '25

24 Apr '25

Dear Colleagues, We are pleased to invite you to an upcoming Metadata Expert Elicitation Session on May 20 2025, at 14:15 CEST. This event is a follow-up to our engaging webinar series last fall, where a presentation on metadata sparked strong interest in further discussion—especially around applications in LMIC settings. This 90-minute session will begin with a brief introduction to key metadata concepts relevant to risk assessments, surveillance, and outbreak response. Following this, participants will join breakout discussions focused on current practices, opportunities for enhancement, and practical challenges in different contexts. The session can be joined by Zoom at: https://dtudk.zoom.us/j/67066262671?pwd=yqMv6duCXRDaSZz6ytH7hVxcV8G3U0.1 Meeting ID: 670 6626 2671 Passcode: 432088 Please email me if you would like me to add you or any of your colleagues to the meeting invite. Warm regards, Christa [cid:image001.png@01DBB518.635D19D0] 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/>

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[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.

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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

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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>

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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>

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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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2026

2025

2024