- Bioinfo List - SeqShare Mailing Lists

Join the Bioinformatics COP now!
by Christa Twyford Gibson 07 Nov '24

07 Nov '24

Hi all, We are kicking off our November Bioinformatics COP now! Please join us online here: Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Cheers, christa [cid:image001.png@01DB3111.5D825830] 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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ONT beats Illumina at variant calling ...
by Marco van Zwetselaar 07 Nov '24

07 Nov '24

... or so the authors* claim in this paper: 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. Weigel D, editor. eLife. 2024;13: RP98300. doi:[10.7554/eLife.98300](https://doi.org/10.7554/eLife.98300) > This important study shows how a combination of the latest generation of Oxford Nanopore Technology long reads with state-of-the art variant callers enables bacterial variant discovery at an accuracy that matches or exceeds the current "gold standard" with short reads. The work thus heralds a new era, in which Illumina short-read sequencing no longer rules supreme. [Source: publisher's assessment, my emphasis.] *) Including bioinformatics superheroes Ryan Wick and Torsten Seemann :) Cheers Marco PS: hope to see you all at the CoP meeting in 2 hours: https://dtudk.zoom.us/j/68365887835

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Metagenomic assemblies tend to break around antibiotic resistance genes
by Marco van Zwetselaar 28 Oct '24

28 Oct '24

Abramova A, Karkman A, Bengtsson-Palme J. Metagenomic assemblies tend to break around antibiotic resistance genes. BMC Genomics. 2024;25: 959. doi:[10.1186/s12864-024-10876-0](https://doi.org/10.1186/s12864-024-10876-0) @Philip I seem to recall a paper from DTU on a tool that tried to solve precisely the issue your eastern neighbours stumble over in this paper? Cheers Marco

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When less is more: sketching with minimizers in genomics
by Marco van Zwetselaar 26 Oct '24

26 Oct '24

Comprehensive overview article on minimizers and how they are used in current tools for alignment, assembly, etc. Great for catching up on some foundational bioinformatics. ;-) Ndiaye M, Prieto-Baños S, Fitzgerald LM, Yazdizadeh Kharrazi A, Oreshkov S, Dessimoz C, et al. When less is more: sketching with minimizers in genomics. Genome Biology. 2024;25:270. https://doi.org/10.1186/s13059-024-03414-4 Cheers Marco

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Updated time for SeqAfrica Bioinformatics Community of Practice: 11:30 UTC/12:30 CET
by Christa Twyford Gibson 23 Oct '24

23 Oct '24

Hi all, Please note the change in time to our monthly SeqAfrica Bioinformatics Community of Practice. We will now be meeting at 11:30 UTC/12:30 CET. We look forward to seeing you at our next meeting on November 7! As always you can find us on Zoom at the link below. Cheers, Christa Christa Gibson is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 [cid:image001.png@01DB2527.3AA13FC0] 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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Reminder: COP tomorrow!!!
by Christa Twyford Gibson 09 Oct '24

09 Oct '24

Dear Colleagues, Just a reminder that our monthly Bioinformatics Community of Practice is TOMORROW 10 October at 13:45 CEST. The Zoom link for the meeting is below! Our colleague Albert Bortey from the Noguchi Memorial Institute for Medical Research will be giving us a demonstration of hARMonize. It should be super interesting! We look forward to seeing you all tomorrow! Christa Christa Gibson is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 [cid:image001.png@01DB1A4A.165EDF60] 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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Change of date for October Bioinformatics Community of Practice: join us on 10 October
by Christa Twyford Gibson 01 Oct '24

01 Oct '24

Dear Colleagues, Please spread the word- we are moving our monthly Bioinformatics COP to 10 October at 13:45 CEST this month. The Zoom link (below) is the same. Please let your colleagues know of the change! Cheers, Christa Christa Gibson is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 [cid:image001.png@01DB134E.CBB49D30] 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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Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050
by Marco van Zwetselaar 18 Sep '24

18 Sep '24

FYI, a new (Wellcome and Fleming funded) comprehensive systematic review of historic & future trends in AMR burden. Naghavi M, Vollset SE, Ikuta KS, et al. Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050. The Lancet 2024; 0. DOI:[10.1016/S0140-6736(24)01867-1](https://doi.org/10.1016/S0140-6736(24)0…. Cited as "39 million estimated deaths from AMR between 2025 and 2050" by Wellcome[1] and HealthData.org[2] Best wishes, Marco [1] https://wellcome.org/news/new-forecasts-reveal-39-million-deaths-will-be-di… [2] https://www.healthdata.org/news-events/newsroom/news-releases/lancet-more-3…

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Fwd: Free online course: Strengthen your antimicrobial resistance prediction skills with experts in bacterial genomics
by Marco van Zwetselaar 13 Sep '24

13 Sep '24

FYI -------- Forwarded Message -------- Subject: Free online course: Strengthen your antimicrobial resistance prediction skills with experts in bacterial genomics Date: Thu, 12 Sep 2024 07:01:12 +0000 From: Wellcome Connecting Science learning and training [<coursesandconferences(a)email.wellcomeconnectingscience.org>](mailto:coursesandconferences@email.wellcomeconnectingscience.org) Reply-To: Wellcome Connecting Science learning and training [<re-6Y2C-RJRY-1ODXOW-C1TZY(a)email.wellcomeconnectingscience.org>](mailto:re-6Y2C-RJRY-1ODXOW-C1TZY@email.wellcomeconnectingscience.org) To: Gain free and expert-led training in AMR genomics and data sharing [View in browser](https://email.wellcomeconnectingscience.org/cr/AQj04xMQ3rlOGNDPrjD… [Wellcome Connecting Science logo] Learning and training [Click this header to find out more about this online course on the FutureLearn website](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg… [Blog](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg88C… [LinkedIn](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjA… [X](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg9cCBD_… [YouTube](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg… Free online training to strengthen your AMR genomics expertise! Dear Marco, [Antimicrobial Resistance and Genotype Prediction: Data Sharing and Analysis](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjA… our free online course led by experts in bacterial genomics and data analysis, focusing on how to use relevant tools and databases for the prediction of antimicrobial resistance (AMR). Starting on 30 September 2024, our educators will guide you through everything you need to learn to confidently predict AMR using your own data, understand effective data-sharing, and enhance your expertise in AMR genomics. The course will run live for three-weeks, during which time you will be able to interact with our educators and other learners (through the FutureLearn platform), and exchange ideas and thinking with peers from across the globe. This is an excellent opportunity for early career researchers, healthcare professionals, and public health experts to benefit from free and accessible training in AMR prediction, using genotypic and phenotypic data, and the latest genomics tools and technologies. Sign up for a free place on the FutureLearn website today, and start learning from 30 September. [Find out more about the course](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg4… Key information Start learning: 30 September 2024 Live period: 3 weeks Weekly study expectation: 5 hours Educators Conor Meehan Nottingham Trent University, UK Jane Hawkey Monash University, Australia Kristy Horan AusTrakka platform, Australia Certificate Gain a certificate on successful completion of the course to demonstrate your learning investment. Free online training to strengthen your AMR genomics expertise! Dear Marco, [Antimicrobial Resistance and Genotype Prediction: Data Sharing and Analysis](#anchor31)is our free online course led by experts in bacterial genomics and data analysis, focusing on how to use relevant tools and databases for the prediction of antimicrobial resistance (AMR). Starting on 30 September 2024, our educators will guide you through everything you need to learn to confidently predict AMR using your own data, understand effective data-sharing, and enhance your expertise in AMR genomics. The course will run live for three-weeks, during which time you will be able to interact with our educators and other learners (through the FutureLearn platform), and exchange ideas and thinking with peers from across the globe. This is an excellent opportunity for early career researchers, healthcare professionals, and public health experts to benefit from free and accessible training in AMR prediction, using genotypic and phenotypic data, and the latest genomics tools and technologies. Sign up for a free place on the FutureLearn website today, and start learning from 30 September. [Find out more about the course](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg5… Key information Start learning: 30 September 2024 Live period: 3 weeks Weekly study expectation: 5 hours Educators Conor Meehan Nottingham Trent University, UK Jane Hawkey Monash University, Australia Kristy Horan AusTrakka platform, Australia Certificate Gain a certificate on successful completion of the course to demonstrate your learning investment. Watch the course trailer to discover more about what you will learn with our expert educators https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAgmsyBD6EIU… https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAgmsyBD6EIU… Learn how to: - Explain the genotypic basis of AMR. - Contrast and critique the various ways to predict AMR from linked genotype and/or phenotype data. - Discuss the various AMR databases, and their related benefits and limitations. - Explain how different AMR prediction tools can be applied, as well as how their outputs are interpreted and implemented. - Explain the current limitations of AMR prediction tools. - Describe the process required to create and share FAIR and open AMR data. Other learning and training events that may interest you [Colour photo of two CRISPR conference delegates discussing scientific poster insights | Image credit: Ben McDade photography for Connecting Science] [Conferences](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDP… [Colour photo of two scientists working in a lab, wearing lab coats and safety gloves, whilst using pipettes | Image credit: Ben McDade photography for Connecting Science] [Courses](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg… [Colour photo of a group of drug discovery course participants in Uruguay | Image credit: Wellcome Connecting Science] [Courses outside the UK](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg-cCBD… Other learning and training events that may interest you [Colour photo of two CRISPR conference delegates discussing scientific poster insights | Image credit: Ben McDade photography for Connecting Science] [Conferences](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDP… [Colour photo of two scientists working in a lab, wearing lab coats and safety gloves, whilst using pipettes | Image credit: Ben McDade photography for Connecting Science] [Courses](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg… [Colour photo of a group of drug discovery course participants in Uruguay | Image credit: Wellcome Connecting Science] [Courses outside the UK](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg-cCBD… [Unsubscribe](https://email.wellcomeconnectingscience.org/uns/AQj04xMQ3rlOGN… | [Forward to an interested colleague](https://email.wellcomeconnectingscience.org/fw/AQj04xMQ3rlOGNDPr… Image credit: Colour photography by Ben McDade for Connecting Science Wellcome Connecting Science Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Reminder: SeqAfrica September Bioinformatics CoP – Exciting AMRomics demo!
by Pernille Nilsson 04 Sep '24

04 Sep '24

Dear Bioinformatics Community of Practice Members, We hope this email finds you well and thriving in your research endeavors! We are excited to inform you of the upcoming Bioinformatics Community of Practice session, where we will be showcasing the AMRomics workflow. This is a fantastic opportunity to see this tool in action and learn how it can enhance your research projects and AMR work. Date: Thursday 5 September Time: 14.00-14.45 CEST Zoom link: https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 During this session, we will demonstrate the key features and capabilities of the AMRomics workflow and engage in a lively Q&A session/discussion to address all your burning questions. This session promises to be informative and fun and it’s a great chance to connect with fellow community members and share insights. Looking forward to seeing you there with your curiosity and enthusiasm. Best wishes, Pernille [signature_1133531634] 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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