Josh Quick

Very excited to get started on my project; OneAMR, which will use single-cell technology to improve the prediction of AMR direct from clinical samples @IMIBirmingham

Looking forward to #ASMicrobe this year!🦠 We've got some great @nanopore events lined up, including an exciting Evening event Friday, June 14th with some of the legends @Scalene, @rrwick, @anna_cusco, @Matt180KDa! Filling up fast, so be sure to register: nanoporetech.com/about/events/c…

First MinION Mk1D sequencing run out in the field! @nanopore #nanoporeconf #10yrsON Taking the sequencer to the samples not the sample to the sequencer.

Job alert 🚨 Research fellow in wastewater surveillance at the University of Birmingham working with myself and @pathogenomenick jobs.ac.uk/job/DFY639/res… This is a read-only post so please email if you have any questions.

Thank you to the Asia PGI for hosting @NetworkArtic as trainers for the first @nanopore sequencing workshop. Amazing teams, flu libraries and metagenomic trouble shooting 🦠🧬🕵️

@PeacockFlu @JosetteSchoenma @theosanderson Yes sequence should start at base 79 for v5.3.2

This tenth BA.2.86 has an extra C21T, T4579A and S:G594S mutation. The one at the bottom of the top branch.

@bioinfomatt @AlexKneubehl @Psy_Fer_ @NetworkArtic @pathogenomenick It's to distinguish between other primers which have been used for that region previously e.g. if you are pooling your own primers.

@AlexKneubehl @Psy_Fer_ @NetworkArtic @Scalene @pathogenomenick It looks like updated code just does this: "Merges a canonical primer site with an alt site, producing an interval that encompasses both" So as long as bed entries have the largest possible region it looks safe just to remove the alt entry and adjust

V5.3.2 @NetworkArtic scheme for SARS-CoV-2 - what is the purpose of the last section of the primer name in the bed file? SARS-CoV-2_31_LEFT_1 - the _1 here @Scalene @pathogenomenick

Only at #CINEMAParis, live @nanopore sequencing run of a zymo mock microbiome by @Scalene next to lighting talk session🔥 We will dive into bioinformatics methods for environmental and clinical microbiome analysis over the next few days ! (Ps. @Scalene said it was a good run!)

PM Day 3 of #imisummerschool2023: Dr Hung-Ji Tsai guided us through the potential reasons for the dinosaurs' demise (clue: recreational fungi were implicated), followed by Dr Josh Quick who took us on a whistle stop tour of Nanopore sequencing. @HJTsai @Scalene @UoBSchool

Last call for this PhD position on wastewater surveillance, closes Friday! findaphd.com/phds/project/p…

If you're at #LC23 check out @chriken_ poster on primer design algorithms!

If I was looking for a PhD right now I'd absolutely apply for this awesome looking one with Josh Quick @Scalene on using nanopore sequencing for pathogen surveillance in wastewater! @IMIBirmingham @UoBbiosciences 🤩 findaphd.com/phds/project/p…

10M reads (N50 30.4kb) on the first run - just time to squeeze in some of our samples before #LC23

Very nice Lambda library by @myxosparkus

We are very excited to have the very first P2 right here in Birmingham. Thanks to all at @nanopore for making it happen!

@mattloose @nanopore That's OK I wanted to sequence Lambda

@Scalene @nanopore Surely lambda?

@chrisnrg @mattloose You are both welcome anytime!

@mattloose No one likes a trip to the worst midlands

Looking forward to seeing this running! Unfortunately that means a visit to Birmingham.

@adampeltan @Scalene @NetworkArtic @DrCJ_Houldcroft Full list now available on the ARTIC blog: community.artic.network/t/artic-multip…

@DrCJ_Houldcroft @adampeltan @NetworkArtic @AnnaKov1988 @igoodfel @PostdocPat No but I've been meaning to add a full list to the blog so I will try and do that.

@adampeltan @Scalene @NetworkArtic I know that @AnnaKov1988 and some of @igoodfel 's team have been working on ARTIC schemes for HCV and HIV, and I'm sure some others as well? There are also schemes designed by Josh and developed by @PostdocPat for even more pathogens.

Hi @Scalene @NetworkArtic Does anyone have a list of all the different pathogens that have been sequenced with the ARTIC multiplex PCR approach? It must be a very long list by now!

@Amandatron89 @beconstant @pvanheus @chriken_ I'm just readying a blog post on the new ARTIC v5 primers

@beconstant @pvanheus @Scalene @chriken_ Perfect thanks. These are omicron isolates from a few months ago anyway so they probably don't need NEW new. We'll go for the ones you're using.

Can someone point me to the most recent version of the Scov2 midnight primers please?