Georgia Breckell

🧬@dwwaite (@MPI_NZ): Rapid ID of Pepino mosaic virus via @nanopore in NZ outbreak 🍅PepMV detected in NZ commercial greenhouse ⚡5-day turnaround for sequencing 🦠CH2 clade & PVX identified 🔬SNP analysis for virulence assessment 🌱Informed real-time response #QRW2024

No. This is not acceptable. The methods section is the single most important part of a scientific paper. If those details are relegated to supplementary materials, then it's not a scientific paper in a scientific journal.

Is @nanopore duplex basecalling beneficial for bacterial genome assembly? I did some tests, and it seems like it might be! New blog post here: rrwick.github.io/2024/05/08/dup…

Intuitive

@m_vlkova Did you solve this? We had a similar query that I ended up solving inefficiently. Would be keen to hear how you did it.

Why does installing cuda on Ubuntu require knowledge of black magic?!

What started as "We'll quickly make some genomes" has turned into a major part of my PhD. Excited to share the latest preprint from the Silander Lab

My top four emojis as a PhD student 😬🙏😭🤯 Seems about right

This is pretty cool - going extinct is a bad thing.

Does it take more time to achieve (computational) reproducibility? No, it's simply that a bit more time is invested up front for easier re-analyses later. Invest in your future self (or your colleague that needs to run your code).

Impressive “the methylation analysis results obtained from a couple of hours of nanopore sequencing matched the pathology results from weeks later”

Listening to @DrKatHolt's and @daanensen's talks makes you wonder about the importance of standardizing genomic data/tools so they can be used for policy decisions. Publishing a manuscript is great, but driving real-time actions is at a different and superior level

I'm very happy to share this review on bioinformatics workflow management systems in @naturemethods If you don't yet use them, please read the review! rdcu.be/cyjRN A bit of background, additional information, and many very special thanks to a lot of people 🧵

I've just released (during #MicroSeq2021) a new short-read polishing tool for fixing errors in long-read bacterial genome assemblies: Polypolish! github.com/rrwick/Polypol… (1/8)

Go to github and press . (full stop) Full blown code editor in the browser on your repo. Basically VSCode. Even if you are an ATOM person (like me) this is very useful when you just wanna do some quick debugging or changes, but not on your "rig". I love it.

New Micro. Res. Announ. paper by @GeorgiaBreckell - if anyone is looking for 47 single-chromosomal-contig soil and water isolates of E. coli, here you are mra.asm.org/content/9/38/e…

@Justin_OGrady @osilander

First attempt at 50 min (from sample to result) CoV test with a 3 min extraction and rapid cycle RT-qPCR on a portable qPCR machine (16 samples per run) with readout on a mobile phone. Needs optimisation but looking promising. Collaboration with Jonathan Edgeworth at St Thomas'

Here's a quick introduction to Snakemake I wrote (including a short section on good old fashioned Make). It tries to clarify some aspects of Snakemake I found confusing early on, and builds up to a SLiM example. vincebuffalo.com/blog/2020/03/0…