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.
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.
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...
New blog post!
I analyse the new [email protected] basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model:
rrwick.github.io/2026/06/11/d...
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...
🎉 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
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/...
Ryan Wick
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...
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...
Linezolid is a critical last-resort antimicrobial for multidrug-resistant Enterococcus faecium , particularly against vancomycin-resistant lineages where therapeutic options are severely limited. Whil...
Introduction. Klebsiella pneumoniae is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages, defined using ...
Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.
AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
