alex

welcome to my website. i'm the one on the left.

[alex @alexomics]

@ZaminIqbal Thank you Zam!

[alex @alexomics]

@The__Taybor @mattloose @nanopore 🙊 I’ll wear @nanopore socks to my next viva

[alex @alexomics]

@mattloose @nanopore And thanks to @ZaminIqbal and @Mark_Ravinet for a great discussion and taking the time to read my thesis

[alex @alexomics]

@mattloose @nanopore Thank you very much, Matt! I definitely couldn’t have done it without your constant support. 🎉

[Matt Loose @mattloose]

We've put out a short preprint today showing some updates in Readfish for @nanopore adaptive sampling. https://t.co/GQJJkIql33 @alexomics is giving a talk shortly at the #nanoporeconf about this - but a short thread here.

[bioRxiv @biorxivpreprint]

Barcode aware adaptive sampling for Oxford Nanopore sequencers. https://t.co/MCah2VFTbE #bioRxiv

[alex @alexomics]

@whelanfj 14 months! That's such a long time! 🤞🏼

[alex @alexomics]

@drjulie_b Fig 1A here: https://t.co/VGWxhJmDEJ ? It's nanopore's 'pore-c' but it's a nice image

[alex @alexomics]

@DrCJ_Houldcroft https://t.co/tZ21NYQ8wq

[alex @alexomics]

@nickdsandy This can also be done using the ont-fast5-api https://t.co/JZ4raecVEP

[Nature Reviews Genetics @NatureRevGenet]

DNA SEQUENCING: Complex targeted sequencing in real time https://t.co/IasiElRA4M #ResearchHighlight

[Oxford Nanopore @nanopore]

If you haven't already, check out this super cool paper from @alexomics and team, describing their new adaptive sampling toolkit Readfish — for enriching targeted panels in human genomic and metagenomic samples:
https://t.co/BcSV4V9l1I

[alex @alexomics]

@miles_benton @CallumJCParr @mattloose If you get a chance, could you open an issue on https://t.co/zrI13GfwH8 ? Just with what you tried/saw. I haven't tried using ARM with this yet, but it'd be good to see if we can get it working

[alex @alexomics]

@osilander @mattloose @nanopore On GPU, with Guppy, yes. I think DeepNano-Blitz only calls DNA at the moment

[Matt Loose @mattloose]

So - our ReadFish paper came out on Monday https://t.co/LWx6m1HHXZ using GPU - but what if you only have a laptop? Here's an update from @alexomics to our tools that enable ReadFish on Mac, Linux or Windows with no additional GPU or compute. https://t.co/CgicPm4nUH for details.

[alex @alexomics]

@luke_earl @mattloose We see 90-95% of reads rejected in 1.2-2 seconds, so roughly 540-900 (ish) bases.

[alex @alexomics]

Very happy to share our work on selective sequencing use the @nanopore MinION. Code is here: https://t.co/iEcFCnR1rb and the paper is here: https://t.co/9KOSnLAl5j

[alex @alexomics]

@drjulie_b Let me know if any of it doesn’t make sense 😊