Sam Wilkinson

Bioinformatician in Loman Labs, UoB.

General purpose NGS data wrangler and CLIMB-COVID administrator.

He / Him

[ARTIC Network @NetworkArtic]

ARTIC #mpox resources! Guides to setup #sequencing #bioinformatics and #analysis

https://t.co/uiPtQgnJwg

@wellcometrust @nanopore @illumina
#molecularepidemiology #pathogen #pathogensurviellance #bioinformatics #epidemiology #virus #outbreak #clinicalvirology

[Sam Wilkinson @BioWilko]

@gaetan_benoit Aw that's a shame, even with the new chemistry and super accuracy basecalling? Q20 in marketing, 98.4% in my tests

[Sam Wilkinson @BioWilko]

@gaetan_benoit I got it running locally with no problem but ran into trouble with containerisation and running with nextflow kubernetes executor unfortunately... I just couldn't get past the dependency check, it's probably just my terrible dockerfile though!

[Sam Wilkinson @BioWilko]

@beconsta Cool, thanks for doing the extra! :)

[Sam Wilkinson @BioWilko]

@beconsta @DrCJ_Houldcroft This is getting dangerously close to *actual * virology.... So I'm going to plead the fifth!

[Sam Wilkinson @BioWilko]

@beconsta @BioMickWatson Maximising human removal would definitely be my priority if I used this, or rather, removing anything that could be even potentially identifiable

[Sam Wilkinson @BioWilko]

@beconsta Also, as a follow-up, it would also be nice to see how effective it is in a worst case scenario when it's trying to throw out human and keep eukaryotic DNA

[Sam Wilkinson @BioWilko]

@beconsta Have you tried testing it with real / simulated human reads from the human pangenome project? My main concern around dehumanisation is around ensuring the equal privacy is provided to all rather than just being very effective at spotting reads from Europeans

[Sam Wilkinson @BioWilko]

@samstudio8 Happy anniversary, the current count is 3,530,744!
The other count (code comments which say "this is horrible, don't @ me" is even higher.....

[Sam Wilkinson @BioWilko]

@Kurz_Gesagt As a biologist I am frankly disappointed with this video, it is factually incorrect on multiple counts and even suggests that credible scientific consensus around the origin of SARS-CoV-2 is split (it isn't) and that controls on synthesising DNA don't exist (they do).

[Sam Wilkinson @BioWilko]

@samstudio8 Who let you out of your cave!?!?!

[Sam Wilkinson @BioWilko]

@OmixLimited Good luck folks!

[Sam Wilkinson @BioWilko]

@andrewwhite01 foo list comp consumes the tuples generator meaning that when the bar list comp tries to do the same it cannot

[Sam Wilkinson @BioWilko]

Omg @AaronPomerantz did I just see you get thanked todays true facts video? Screw nature papers, that's how you know you've made it 😁
https://t.co/MJPJoNtRZZ

[Mike Cox @MikeyJ]

Also a reminder about our *NEW* MRes in Microbial Genomics - please share with your undergrads. It aims to train genomics literate microbiologists, applications are open and I'm happy to be contacted directly to discuss. https://t.co/2EbZOgsDsd

[Josh Quick @Scalene]

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

[Andrew Page @andrewjpage.bsky.social @andrewjpage]

Thanks to everyone for coming to the Microbes & Food Safety Bioinformatics Hackathon. The main takeaway is that ChatGPT is coming fast and will fundamentally change how bioinformatics is performed

[Sam Wilkinson @BioWilko]

Goodness me, Cambridge is rather fancy @unibirmingham need to up your game