Ryan Wick

No longer active here. Find me on Bluesky:

[Ryan Wick @rrwick]

This will be my last post here. I'm moving to Bluesky:
https://t.co/bEO2oU2KA5

Hope to see you there!

[Ryan Wick @rrwick]

To make producing soft core alignments easier, we developed Core-SNP-filter, a simple and efficient tool to process SNP alignments with user-defined thresholds.
https://t.co/Vyny4agUQk
(4/4)

[Ryan Wick @rrwick]

Do you make core genome alignments for phylogenomics? @monaltaouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets.
https://t.co/WnmQuLFkwj
(1/4)

[Ryan Wick @rrwick]

And the benefits grow with dataset size! A 100% strict core may work fine for small datasets (e.g. ~10 genomes) but is devastating for very large ones (e.g. 1000+ genomes). A 95% soft core works well across all dataset sizes.
(3/4)

[Ryan Wick @rrwick]

@krannich479 You can certainly give it a try, but linear sequences can be challenging for Autocycler at the moment (a focus for future development), so if your viral genome is not circular, it may not be a great fit.

[Ryan Wick @rrwick]

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: https://t.co/NksiyESF7u
(1/5)

[Ryan Wick @rrwick]

Autocycler is still new and evolving. I'll continue to improve it based on your feedback. A big thank you to the alpha testers who gave me feedback before this release! Give it a try and share your thoughts.
(5/5)

[Ryan Wick @rrwick]

However, Autocycler still allows users to manually intervene when they would like to. So it aims for the best of both worlds: either hands-off automated assemblies or hands-on curated assemblies, as the user sees fit.
(4/5)

[Ryan Wick @rrwick]

@Mr100years @nanopore Yup: https://t.co/P6P5OmbopB

[Ryan Wick @rrwick]

Just had my first experience with CycloneSEQ data and shared my findings in this blog post:
https://t.co/70UrEkdC4N

How does CycloneSEQ compare to @nanopore? I looked at both read-level and consensus-level accuracy. Check it out!

[George Bouras @GB13Faithless]

If you want to try out the new --bacteria Medaka polishing option after reading Ryan's thoughts in his latest blogpost, the newest Hybacter v0.10.0 release now includes it as the default

https://t.co/YvgSurzg36

[Ryan Wick @rrwick]

A little bit overdue, but here are my thoughts on @nanopore's recent release of Medaka:
https://t.co/SNYrZczPad

[Marit Hetland @genomarit]

Excited to share this preprint where we’ve used genomic analysis of >3000 genomes to study Klebsiella pneumoniae in a One Health perspective 🦠🔬👩‍💻#OneHealth #KLEBGAP #KlebClub @IrenLohr @DrKatHolt @NORKLEBNET

[Ryan Wick @rrwick]

Our OnION sequencing computer now has a little sibling: Spring OnION!

Short post with some stats and benchmarks: https://t.co/St8kaw0bGi

[Ryan Wick @rrwick]

@martinalexsmith @nanopore If you're assembling hac reads, then make sure to run Medaka. I've found it's much more beneficial for hac-based assemblies than for sup-based assemblies.

[Ryan Wick @rrwick]

I finally got around to testing HERRO (https://t.co/irsWGnjpT2), the new @nanopore read correction algorithm which takes simplex ONT reads to PacBio-HiFi-level accuracy.

I was impressed! Findings are on my blog in a two-part post:
https://t.co/unWf7fIMFS
https://t.co/yEllyimky8

[Microbiology Society @MicrobioSoc]

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies. Published #OpenAccess and fee-free in #MGen using a #PublishAndRead agreement: https://t.co/DSPZ4EFUK2