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

GitHub - rrwick/Polypolish: a short-read polishing tool for long-read assemblies

a short-read polishing tool for long-read assemblies - rrwick/Polypolish

github.com

New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)

In some recent blog posts, I had a Klebsiella genome with a mysteriously higher ONT error rate. But Michael Biggel (University of Zurich) emailed me with the likely explanation: 7-deazaguanine mods. Thanks, Michael! Here's his preprint about this: www.biorxiv.org/content/10.6...

Standalone nanopore sequencing for foodborne pathogen surveillance: a large-scale evaluation and quality control framework

Whole-genome sequencing (WGS) is central to foodborne pathogen surveillance and cross-border outbreak detection. Long-read sequencing using Oxford Nanopore Technologies (ONT) promises rapid, complete,...

biorxiv.org

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

agtools: A Software Framework to Manipulate Assembly Graphs

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

academic.oup.com

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...

Novel transposon Tn8026 acts as a global driver of transmissible linezolid resistance in Enterococcus via a linear plasmid

Linezolid is a critical last-resort antimicrobial for multidrug-resistant Enterococcus faecium , particularly against vancomycin-resistant lineages where therapeutic options are severely limited. Whil...

medrxiv.org

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...

Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages

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 ...

microbiologyresearch.org

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/...

Protein structure-informed bacteriophage genome annotation with Phold

Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.

academic.oup.com

George Bouras@gbouras13.bsky.social · 12mo ago

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...

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.

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

Autocycler: long-read consensus assembly for bacterial genomes

AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

doi.org

New blog post! metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper: rrwick.github.io/2025/09/23/a... Both tools improved considerably! Time to update your conda environments 😄

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

agtools: a software framework to manipulate assembly graphs

Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler to construct longer genomic f...

biorxiv.org

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

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 11mo ago

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

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...

Minor new release of @nanoporetech.com's Dorado: github.com/nanoporetech... It supports using --bacteria when polishing an assembly with v5.2.0 data, which is nice! But if I understand correctly, it's the same bacterial polishing model from Sep 2024, not a new model.

A new long-read metagenome assembler has been released: myloasm. Very exciting! Looking forward to trying it out.

Jim Shaw@jimshaw.bsky.social · last yr.

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

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.

Release v1.0.0 · nanoporetech/dorado

[1.0.0] (21 May 2025) We are pleased to announce the release of Dorado v1.0, delivering new models and capabilities for Oxford Nanopore data analysis. This release introduces: New v5.2 basecalling...

github.com

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

Autocycler: long-read consensus assembly for bacterial genomes

Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...

biorxiv.org

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...

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them? If so, you might this little project: github.com/rrwick/conda...

GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions

a simple tool for listing conda environments with descriptions - rrwick/condaenvlist

github.com

New preprint is out! We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling. Read it here: www.biorxiv.org/content/10.1... Data & code: github.com/rrwick/Are-r... (1/8)

Are reads required? High-precision variant calling from bacterial genome assemblies

Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...

biorxiv.org

I re-ran previous ONT basecalling benchmarks using the latest version of Dorado (thanks, @vellamike.bsky.social), and the RTX 40 series GPUs show an impressive speed boost! Check out the updated benchmark results at the bottom of this post: rrwick.github.io/2024/08/16/s...