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Benchmarking short and long read polishing tools for Nanopore assemblies
by Marco van Zwetselaar 17 Jul '24

17 Jul '24

Thorough evaluation of Nanopore assembly polishers: Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10582-x Best wishes, Marco

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Reminder: SeqAfrica Bionformatics Community of Practice this Thursday at 14:00 CEST
by Christa Twyford Gibson 02 Jul '24

02 Jul '24

Dear Colleagues, We are looking forward to the next commiunity of practice session to take place this Thursday at 14:00 CEST! We will have a special guest host, Niamh Lacy-Roberts, who will discuss the results of SeqAfricas's recent optimization experiments for ONT sequencing. In particular, she will cover testing various input concentrations and multiplexing different numbers of isolates using the rapid barcoding kit. The focus of the experiments was to determine the best combination that yields the highest sequence quality, enabling accurate typing (MLST, AMR genes etc) and cluster analysis. She will also go over the tools used to analyze the ONT data. You can join the meeting here: Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 We look forward to seeing you Thursday! Kind Regards, Christa [cid:image001.png@01DACC7E.F37D4630] 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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HAMRonization tool + slides from today's COP
by Christa Twyford Gibson 06 Jun '24

06 Jun '24

Hi all, For those who missed today's SeqAfrica Bioinformatics Community of Practice meeting, I wanted to share the slides that Marco presented. I've also shared below a link to an interesting article about a new tool developed by PHAG4E called hAMRonization. It is one of the tools that Marco shared with us in the COP meeting today. hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling | bioRxiv<https://www.biorxiv.org/content/10.1101/2024.03.07.583950v1> Cheers! Christa [cid:image001.png@01DAB820.47C52E60] 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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Fwd: Reminder to register | Genomic surveillance of pathogens | Frontiers Forum webinar
by Marco van Zwetselaar 29 May '24

29 May '24

Dear all, FYI. Registration is open: https://fro.ntiers.in/znQ6 Kind regards, Marco -------- Forwarded Message -------- Subject: Reminder to register | Genomic surveillance of pathogens | Frontiers Forum webinar Date: Wed, 29 May 2024 09:44:59 +0000 From: Laure Sonnier | Frontiers Forum [<fsci(a)events.frontiersin.org>](mailto:fsci@events.frontiersin.org) To: [89aa0f9662f81a2d5fda6d72096f3727.FSCI_Forum_Net-Zero_Siegert_Deep-dive_Bann… Dear Marco, Don't miss this complimentary Frontiers Forum Deep Dive webinar on 5 June to discuss technologies and enablers for global surveillance of infectious diseases and antimicrobial resistance. The event is led by the former Chief Microbiologist at the European Centre for Disease Prevention and Control (ECDC), Prof Marc Struelens. Marc is joined by expert panel members Prof Vitali Sintchenko, Prof Guido Werner, Prof Margaret Ip, Dr Stephen A Morse, and Dr Josefina Campos. [Register](http://email.events.frontiersin.org/c/eJxszL9q6zAUgPGnkTabo_PHtgY… [Decline](http://email.events.frontiersin.org/c/eJxszL1u7CAQQOGngc7WMAx_BcWV… This interactive webinar builds on a recent Frontiers in Science article advocating for the integration of pathogen genomic data and epidemiological data into globally interconnected One Health surveillance systems. [Read the article](http://email.events.frontiersin.org/c/eJxczjGO6yAQgOHTQBc0zAwGCorX… The article authors and panelists will explore the latest advances in whole genome sequencing of pathogens, and the next steps for deploying real-time genomic surveillance to protect us from future pandemics. You can pose questions to the panel during the audience Q&A. I look forward to the discussion on 5 June. Kind regards, [bc5daef97e935cf7716a1e91a3edec64.Laure-Sonnier.png](http://email.events.fro… Frontiers Forum Deep Dive sessions bring researchers, policy experts, and innovators together from around the world, to discuss a specific area of transformational science published in Frontiers' flagship, multidisciplinary journal,[ Frontiers in Science](http://email.events.frontiersin.org/c/eJxcyrFywyAMANCvgS0-kASYQUMX…, and explore next steps for the field. [Privacy Policy](http://email.events.frontiersin.org/c/eJxcyrGSgyAQANCvgU5nWXYVCopr_… | [Manage your email preferences](http://email.events.frontiersin.org/c/eJxcy0Fz1CAYxvFPA7fNwAsE… [Unsubscribe](http://email.events.frontiersin.org/c/eJxUjc1q8zAQAJ9GusWsdld_…

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Soapbox talk for June meeting
by Marco van Zwetselaar 26 May '24

26 May '24

Dear all, Who of you would be up for a brief talk in the June CoP Bioinformatics meeting? The idea of the "soap box" is that you get to talk (for 10-20mn) about something you've been working on / looking into / essentially anything that could be of interest to fellow bioinformaticians. The meeting will be on 6 June at noon UTC, so there's time to think something up! :-) Cheers Marco

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WHO bacterial priority pathogens list 2024
by Marco van Zwetselaar 23 May '24

23 May '24

The WHO bacterial priority pathogens list 2024 has been issued: https://www.who.int/publications/i/item/9789240093461 Greetings, Marco

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AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance
by Marco van Zwetselaar 20 May '24

20 May '24

Another candidate for the AMR genomics toolbox. Nice graphics for sure. And @Christa: they claim it works for Nanopore reads as well. :) Le, D.Q., Nguyen, S.H., Nguyen, T.T. et al. AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance. BMC Bioinformatics 25, 193 (2024). https://doi.org/10.1186/s12859-024-05792-9 Cheers, Marco

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Concordance of genotypic AMR prediction and lab AST
by Marco van Zwetselaar 16 May '24

16 May '24

Dear all, Does anyone have pointers to studies on the concordance of (our) genotypic AMR predictions and actual lab AST results? When I was at KCRI, we did one such analysis but only for our small collection of Acinetobacters[1]. What I would be interested in is a systematic large scale analysis. As the SeqAfrica consortium (and with other partners in & outside Africa), we should have plenty of data to do such a study. My interest in this used to be due to the obvious reason that we need to know how good our predictions are, but there's a much more compelling reason now to gather an extensive collection of *false negatives*. I'll explain later. Marco [1] https://academic.oup.com/jac/article/74/6/1484/5370329

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Are we missing novel resistance genes?
by Marco van Zwetselaar 14 May '24

14 May '24

Dear all, I think with this final question I have covered all the open ends from the CoP meeting. Please drop anything I missed on the list! This interesting question was brought up by several people in the meeting: to what extent are we able to detect novel resistance genes (or virulence genes, or plasmids)? Given that our current tools are all based on mapping sequence data on reference databases, to what extent does this generalise beyond relatively similar sequences? An obvious direction to look in are deep learning models, which appear to have a remarkable capacity to generalise beyond their training data - but could they actually predict genes coding for a hitherto unknown resistance mechanism, or even predict resistance for a highly diverged gene, while never having seen the phenotypic "ground truth"? This explains my interest in the concordance of genotypic prediction and phenotypic AMR, and collecting the false negatives: isolates with positive AST but negative ResFinder prediction are precisely the ones we'd like to be able to generalise to! In my very limited experience (we did one study in 2021, looking at GPlas / MLPlasmid and Deeplasmid for predicting plasmids), the tools essentially predicted (poorly) what was already in the PlasmidFinder database. Clearly though there has been a lot of development since, and I would be very interested to hear of your experiences! Marco

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Parameter settings question
by Marco van Zwetselaar 14 May '24

14 May '24

Dear all, With internet connectivity seemingly returning to East Africa, I'll spam the list with some more questions that came up in the CoP meeting. Here's the next. When running tools like ResFinder and VirulenceFinder, I generally rely on their default cut-off settings (usually: 60% coverage, 90% identity). Is there an empirical basis for these settings or did someone just pull them out of thin air? Do the default settings suffice or should we be more judicious? Perhaps use different settings for different species, different AMR genes, when testing on reads vs assemblies? Marco

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2026

2025

2024

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