There were so many great updates at London Calling #nanoporeconf this year -- here's a selection I found particularly exciting for the field of microbial genomics 🦠 with the latest Oxford Nanopore announcements (a thread 🧵)

🧬 Exciting milestone! Initiated bacterial WGS at the NIH Pakistan using cutting-edge v14 chemistry on R10.4.1 flow cells. This wouldn't have been possible without invaluable guidance and support from the Benjamin Howden team and CEO NIH.Sarah L Baines Claire Gorrie Louise Judd

New blog post: rrwick.github.io/2024/06/11/sho… ONT-only bacterial assemblies are much better than they were only a couple of years ago. Often <10 errors in the whole genome. Does that mean that less short-read sequencing is required for polishing? See my post for the answer! (1/4)

Great talk by Ryan Wick at the Oxford Nanopore event on Perfect Genome Assemblies. If you drink the Kool-Aide they are serving here - there’s no need for Illumina for anymore. #asmicrobe

PulseNet Asia Pacific ONT training has started. In collaboration with ⁦Doherty Institute⁩ ⁦CDC⁩ ⁦APHL⁩ ⁦Oxford Nanopore⁩

Very pleased to say that our preprint investigating CRISPR-Cas9 enrichment of Enterobacterales pathogens is now public! We enriched for tRNA, MLST, AMR and integron genes and sequenced on Oxford Nanopore platforms (1/8). biorxiv.org/content/10.110…

Happy to see this paper out from my PhD student Hugh Cottingham! Huge amount of work here developing methods to use CRISPR to enrich for Klebs on the ONT platform

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies. Published #OpenAccess and fee-free in #MGen using a #PublishAndRead agreement: doi.org/10.1099/mgen.0…

I finally got around to testing HERRO (github.com/lbcb-sci/herro), the new Oxford Nanopore read correction algorithm which takes simplex ONT reads to PacBio-HiFi-level accuracy. I was impressed! Findings are on my blog in a two-part post: rrwick.github.io/2024/07/26/her… rrwick.github.io/2024/07/31/her…

Our OnION sequencing computer now has a little sibling: Spring OnION! Short post with some stats and benchmarks: rrwick.github.io/2024/08/16/spr…

Ryan Wick Someone Oxford Nanopore should make sure you get a #mk1d to join the family 😉

Representing a lot of hard work from Ninin UoN LongRead John Tyson Deep Seq Josh Quick and Nick Loman pleased to share biorxiv.org/cgi/content/sh… which captures all our experience with ultra long read sequencing on Oxford Nanopore - a lot has happened since @scalene first generated ultras!

Hey Oxford Nanopore why can’t we get MinION starter packs and P2 solos into Asia Pacific and Africa any more?

(1/6) Our new short preprint, led by Helena Cooper and myself on incidental bacterial domestication between patient isolation and creation of frozen stock. Geno/phenotype changes are obscured by rich media and more prevalent than we previously thought biorxiv.org/content/10.110…

“This important study shows how a combination of the latest generation of Oxford Nanopore 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” elifesciences.org/articles/98300

🦠🔬An international team of researchers has found that an antibiotic commonly prescribed for patients with liver disease, has led to the global emergence of an almost untreatable form of antimicrobial resistant superbug. go.unimelb.edu.au/4zg8 UniMelb MDHS The Royal Melbourne Hospital

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autocyc… (1/5)

🧵1/ We are excited to share our Nature Communications piece where we explore methods for #onehealth genomic epidemiology and identify links between humans, animals, wildlife, food and the environment. Check it out here - rdcu.be/d5oTo. Doherty Institute Australian Institute for Microbiology & Infection

This week, we established a new Grant Programme to support researchers who are pursuing breakthrough science but may lack all the resources to access Oxford Nanopore sequencing. Find out more and how you can apply here: register.nanoporetech.com/grants-program… #AnythingAnyoneAnywhere

Last week we had an action packed agenda visiting our World Health Organization (WHO) IPSN Catalytic Grant Salmonella/Shigella #WGS #AMR project partners at MRI, Sri Lanka 🇱🇰 A full week of training, site visits and impactful policy meetings. Thanking Dr Sujatha and MRI for the amazing hospitality🧬👩🏻‍🔬