- Bioinfo List - SeqShare Mailing Lists

ONT Knowledge Exchange
by Christa Twyford Gibson 29 Aug '24

29 Aug '24

Hi all, Please see the link below for an upcoming knowledge exchange hosted by ONT. Webinar: sequencing and analysis of nanopore-only microbial isolates (nanoporetech.com)<https://nanoporetech.com/about/events/knowledge-exchange/sequencing-and-ana…> I hope some can join! Cheers, Christa [cid:image001.png@01DAFA58.6AAD76B0] 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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Yet another AMR pipeline: AMRomics
by Marco van Zwetselaar 31 Jul '24

31 Jul '24

AMRomics: a scalable workflow to analyze large microbial genome collections https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10620-8 Two interesting features (vis a vis other pipelines): support for Nanopore reads, and construction of phylogenetic trees from core-genomes of the data. Cheers, Marco

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Reminder: Bioinformatics COP this Thursday!
by Christa Twyford Gibson 30 Jul '24

30 Jul '24

Dear Colleagues, Don't forget this month's SeqAfrica Bioinformatics Community of Practice meeting! We will be discussing new developments in sequencing and bioinformatics tooling for microbial / AMR genomics. The meeting is Thursday (1.8.24) at 14:00 CEST. The zoom link is below. We can't wait to see and hear from you! Please share this invitation with your bioinformatics-curious and interested friends! Kind Regards, Christa Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 [cid:image001.png@01DAE276.7B716BE0] 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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... and yet another plasmid finder
by Marco van Zwetselaar 30 Jul '24

30 Jul '24

PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning https://doi.org/10.1093/bib/bbae322 Cheers, Marco

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BLAST core_nt to be default from Aug 1st
by Marco van Zwetselaar 24 Jul '24

24 Jul '24

NCBI announces the "better, faster, smaller" core_nt database to become the default from August: From: NLM/NCBI List blast-announce [<blast-announce(a)ncbi.nlm.nih.gov>](mailto:blast-announce@ncbi.nlm.nih.gov) Interested in faster nucleotide BLAST searches with more focused search results? NCBI has been re-evaluating the BLAST nucleotide database (nt) to make it smaller and more efficient. Thanks to your feedback, we have created the core nucleotide database (core_nt), an alternative to the default nt database that contains better-defined content and is less than half the size. Read more at NCBI Insights and try out the new database: https://bit.ly/46d49r8 https://bit.ly/46d49r8

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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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2025

2024