Georgia Breckell

Bioinformatician currently developing cutting-edge High-throughout sequencing diagnostic methods in a biosecurity context 🦠🧬🧫🔬💻

[Rhys White 🧬 @RhysTWhite]

🧬@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

[Peter Tennant has moved to Bluesky @PWGTennant]

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.

[Ryan Wick @rrwick]

Is @nanopore duplex basecalling beneficial for bacterial genome assembly? I did some tests, and it seems like it might be!

New blog post here:
https://t.co/4nUVbhgQZy

[Georgia Breckell @GeorgiaBreckell]

Intuitive

[Lucy Furfaro @Lucyleef]

The best explanation of phylogeny I've seen 🤣 @torstenseemann takes us through bioinformatics applications at #ECCMID2024

[Georgia Breckell @GeorgiaBreckell]

@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.

[Sasha Luccioni, PhD 🦋🌎✨🤗 @SashaMTL]

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

[Georgia Breckell @GeorgiaBreckell]

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

[Olin Silander @osilander]

New preprint on benchmarking hybrid assemblies for bacterial genomes, all due to the hard work of @GeorgiaBreckell https://t.co/KpkFel3iSg. A couple years of work, 17 flow cells, and >100 Gbp of data.

[Georgia Breckell @GeorgiaBreckell]

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

[Kathy Belov @KathyBelov]

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

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

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).

[Gang Fang @gangfang_1]

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

[Sergi Arredondo @Sergi_Arredondo]

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

[Jonathan Göke @JonathanGoeke]

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! https://t.co/9I4gMexcsh A bit of background, additional information, and many very special thanks to a lot of people 🧵

[Ryan Wick @rrwick]

I've just released (during #MicroSeq2021) a new short-read polishing tool for fixing errors in long-read bacterial genome assemblies: Polypolish!
https://t.co/6eWZuWJQmp
(1/8)

[James Ferguson @Psy_Fer_]

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.

[Olin Silander @osilander]

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 https://t.co/TRgNMCADPK

[Georgia Breckell @GeorgiaBreckell]

@Justin_OGrady @osilander

[Vince Buffalo @vsbuffalo]

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. https://t.co/4w3Df9uotz