Bioinfo List May 2024

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6 participants
12 discussions

Minutes of CoP Bioinformatics meeting
by Marco van Zwetselaar 13 May '24

13 May '24

Dear all, Greetings from a mostly disconnected East Africa[*]! Thanks all who attended the CoP Bioinformatics meeting last week. I think a lot of interesting points were brought up. Rather than distributing a document with minutes, let me send out a string of emails (one per topic, for easier follow-up) with open ends that were brought up. Do chime in if you have additions or answers! Ahead of this, here's my recollection of activities mentioned in the "stand-up round", i.e. things that people are working on / would like to learn more about / will be working on: - Streptococcus pneumoniae pipeline - Klebsiella pneumoniae, hypermucous - Hybrid Illumina / Nanopore assembly - Novel sequence types found in clinical isolates - New resistance genes - Vaccination targets - Standardised cut-offs for detection - QA, assembly quality analysis - Repeated sequences detection - Evolutionary biogenetics - Microbial metagenomics Kind regards, Marco [*] Apparently there was a break in the deep sea connection to South-Africa yesterday morning, and most East African internet traffic is now being redirected through Madagascar - at crawling speed. Good to see that old fashioned email still mostly makes it through! :-)

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ONT pipeline question (again)
by Christa Twyford Gibson 13 May '24

13 May '24

Hi Bioinformatics Community of Practice Members, Now that we have more members on this listserv, I thought I’d ask this question one more time. 😊 SeqAfrica wants to set up an expert elicitation to talk about harmonization and standardization of tools for MinION data analysis and we need your input! Please respond with the answer to this question: If you conduct viral and/or microbial sequencing using an Oxford Nanopore Technologies sequencing platform, what pipeline do you use for analysis? We will invite the developers of the most used pipelines to speak at an upcoming workshop! Thank you for your input! Christa [cid:image001.png@01DAA51C.4620C130] Christa Twyford Gibson Project Manager for SeqAfrica Project SEQAFRICA (antimicrobialresistance.dk)<https://antimicrobialresistance.dk/seqafrica.aspx> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 935 106 61 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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