Ryan Wick

Polypolish v0.7.1 is out! github.com/rrwick/Polyp... Main new feature is better handling of read name suffixes, which makes it easier to use Polypolish with aligners other than BWA-MEM. I've been using it with minibwa, which seems pretty great: github.com/lh3/minibwa

Follow-up to my last two blog posts: I now look at methylation calling with Dorado v2 and the new hac@v6.0.0 model from @nanoporetech.com. rrwick.github.io/2026/07/08/d...

Follow-up to my last blog post: I now look at assembly polishing with Dorado v2 and the new hac@v6.0.0 model from @nanoporetech.com. rrwick.github.io/2026/06/19/d...

New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

🎉 Excited to share that our paper, “agtools: A Software Framework to Manipulate Assembly Graphs”, has been accepted in Bioinformatics Advances. (1/n) 🔗 GitHub: github.com/Vini2/agtools 📄 Paper: academic.oup.com/bioinformati... #bioinformatics #genomics #openscience

Excited to finally share our new preprint on bioRxiv describing Verticall (github.com/rrwick/Verti...), a robust & efficient tool for building recombination-free bacterial phylogenies. Huge thanks to @rrwick.bsky.social & @katholt.bsky.social for this incredible work! www.biorxiv.org/content/10.6...

Until joining @loolibear.bsky.social's lab in July, I embarrassingly hadn't had much experience with plasmids. So when I started, Leah said "here you go, have a look at this dataset". What a fun ride this has been. Preprint out today and thread below www.medrxiv.org/content/10.6...

New blog post: ONT read QC strategies for assembly rrwick.github.io/2026/02/05/r... Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.

Our new paper on Insertion Sequences (IS) in #Klebsiella - Lineages have vastly different IS loads and profiles - An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution. www.microbiologyresearch.org/content/jour...

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued: rrwick.github.io/2026/01/21/p...

Just updated this old blog post: rrwick.github.io/2023/04/19/v... Now uses qsv instead of xsv, plus some other miscellaneous tweaks/fixes. In the 2+ years since I wrote this post, I use my tv function a LOT.

Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n) www.biorxiv.org/content/10.1... #Bioinformatics #genomics #assembly #assemblygraphs #software

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

New blog post! I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising. Check it out here: rrwick.github.io/2025/09/04/h...

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1 www.medrxiv.org/content/10.1...

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

New version of Dorado is out: github.com/nanoporetech... And for the first time in a year, this includes new DNA basecalling models! I'll try out these new models (v5.2.0) and compare them to the previous ones (v5.0.0) in a blog post in the near future.

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...