Ryan Wick

This will be my last post here. I'm moving to Bluesky: bsky.app/profile/rrwick… Hope to see you there!

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. github.com/rrwick/Core-SN… (4/4)

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)

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. microbiologyresearch.org/content/journa… (1/4)

@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.

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: github.com/rrwick/Autocyc… (1/5)

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)

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)

@Mr100years @nanopore Yup: rrwick.bsky.social

@rrwick @nanopore Thanks for this! Have you enrolled on Blue Sky? If so could you also post this there?

Just had my first experience with CycloneSEQ data and shared my findings in this blog post: rrwick.github.io/2024/12/17/cyc… How does CycloneSEQ compare to @nanopore? I looked at both read-level and consensus-level accuracy. Check it out!

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 github.com/gbouras13/hybr…

A little bit overdue, but here are my thoughts on @nanopore's recent release of Medaka: rrwick.github.io/2024/10/17/med…

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

Our OnION sequencing computer now has a little sibling: Spring OnION! Short post with some stats and benchmarks: rrwick.github.io/2024/08/16/spr…

@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.

Any one else keen to see the practical impact of @nanopore basecaller updates on human/bacterial reference samples? I'm still uncertain if SUP is (pragmatically) worth the extra time & electrons. github.com/nanoporetech/d…

I finally got around to testing HERRO (github.com/lbcb-sci/herro), 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: rrwick.github.io/2024/07/26/her… rrwick.github.io/2024/07/31/her…

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: doi.org/10.1099/mgen.0…