April 2024 - Bioinfo List - SeqShare Mailing Lists

Many purported pseudogenes in bacterial genomes are bona fide genes
by Marco van Zwetselaar 29 Apr '24

29 Apr '24

Dear all, I found this an interesting read: Cooley, N.P., Wright, E.S. Many purported pseudogenes in bacterial genomes are bona fide genes. BMC Genomics 25, 365 (2024). https://doi.org/10.1186/s12864-024-10137-0 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10137-0 It's actually more about assembly quality (and its factors) than about pseudogenes as such. I like their idea that pseudogene count could be used as an indicator of genome quality. Makes sense if you consider that it is biologically improbable to find a pseudogene where the closest reference has a functional gene. Marco

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ONT pipeline tools
by Christa Twyford Gibson 18 Apr '24

18 Apr '24

Hi Bioinformatics Community of Practice Members, 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@01DA917D.D7B2F4E0] 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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Bioinfo-list finally LIVE!
by Marco van Zwetselaar 14 Apr '24

14 Apr '24

Dear all, This took a while to get right, but finally we are up and running! This mailing list was set up for the SeqAfrica Bioinformatics Community of Practice, but is open to all bioinformaticians with an interest in microbial (AMR) genomics. The bioinfo-list is publicly archived at [1] (where you are probably reading this). To subscribe, send an email to bioinfo-list-join(a)seqshare.org or visit [2]. Kind regards, Marco [1] https://lists.seqshare.org/archives/list/bioinfo-list@seqshare.org/ [2] https://lists.seqshare.org/mailman/lists/bioinfo-list.seqshare.org/

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2025

2024

Bioinfo List April 2024