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Ryan Wick

@rrwick.bsky.social

1.2K followers 127 following 95 posts

Bioinformatician at the Centre for Pathogen Genomics at the University of Melbourne

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Ryan Wick @rrwick.bsky.social · 29/07/2026

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

Ryan Wick @rrwick.bsky.social · 24/07/2026

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

rrwick.github.io

Benchmark update: Ilesta, Autocycler-fast and new versions

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 09/07/2026

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,...

Ryan Wick @rrwick.bsky.social · 08/07/2026

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...

rrwick.github.io

Dorado v2.0.0 part 3: methylation

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 19/06/2026

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...

rrwick.github.io

Dorado v2.0.0 part 2: assembly polishing

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 11/06/2026

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...

rrwick.github.io

Dorado v2.0.0: no more sup?

a blog for miscellaneous bioinformatics stuff

Reposted by Ryan Wick

Vijini Mallawaarachchi @vijinim.bsky.social · 08/05/2026

🎉 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

academic.oup.com

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

Reposted by Ryan Wick

Erkison Odih @erkison.bsky.social · 27/04/2026

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...

Reposted by Ryan Wick

Michael Hall @mbhall88.bsky.social · 05/03/2026

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...

Ryan Wick @rrwick.bsky.social · 05/02/2026

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.

rrwick.github.io

ONT read QC strategies for assembly

a blog for miscellaneous bioinformatics stuff

Reposted by Ryan Wick

Ben Vezina @bananabenana.bsky.social · 22/01/2026

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...

microbiologyresearch.org

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 ...

Reposted by Ryan Wick

George Bouras @gbouras13.bsky.social · 14/01/2026

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/...

academic.oup.com

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.

Ryan Wick @rrwick.bsky.social · 21/01/2026

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...

rrwick.github.io

P2 Solo announcement and the trade-offs of a more stable ONT

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 13/01/2026

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.

rrwick.github.io

Viewing tables on the command line

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 29/09/2025

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

Ryan Wick @rrwick.bsky.social · 23/09/2025

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 😄

rrwick.github.io

Benchmark update: metaMDBG and Myloasm

a blog for miscellaneous bioinformatics stuff

Reposted by Ryan Wick

Vijini Mallawaarachchi @vijinim.bsky.social · 17/09/2025

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...

Reposted by Ryan Wick

Jim Shaw @jimshaw.bsky.social · 08/09/2025

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

Ryan Wick @rrwick.bsky.social · 04/09/2025

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...

rrwick.github.io

Cross-sample homopolymer polishing with Pypolca

a blog for miscellaneous bioinformatics stuff

Reposted by Ryan Wick

Hugh Cottingham @hughcottingham.bsky.social · 30/07/2025

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...

Ryan Wick @rrwick.bsky.social · 10/06/2025

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.

Release v1.0.1 · nanoporetech/dorado

[1.0.1] (4 June 2025) This release introduces support in the --bacteria mode of Dorado polish for data basecalled with v5.2 models and improves the speed of 5mCG_5hmCG calling with v5.0 and v5.2 mo...

Ryan Wick @rrwick.bsky.social · 29/05/2025

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

Reposted by Ryan Wick

Jim Shaw @jimshaw.bsky.social · 28/05/2025

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

myloasm-docs.github.io

myloasm - metagenomic assembly with (noisy) long reads

Ryan Wick @rrwick.bsky.social · 27/05/2025

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...

rrwick.github.io

Dorado v1.0.0 and the v5.2.0 basecalling models

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 22/05/2025

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...

Ryan Wick @rrwick.bsky.social · 21/05/2025

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...

Reposted by Ryan Wick

Zamin Iqbal @zaminiqbal.bsky.social · 19/05/2025

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...

Ryan Wick @rrwick.bsky.social · 27/03/2025

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

Ryan Wick @rrwick.bsky.social · 03/03/2025

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...

Ryan Wick @rrwick.bsky.social · 21/02/2025

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...

rrwick.github.io

Spring OnION: a high-spec laptop for ONT sequencing

a blog for miscellaneous bioinformatics stuff

Reposted by Ryan Wick

Mike Vella @vellamike.bsky.social · 20/02/2025

Dorado now supports bacterial genome polishing. It can output assemblies in FASTQ, including Q scores. @rrwick.bsky.social 's analysis shows Q scores are well correlated with base call reliability, meaning they can help reduce false positives in variant calling. rrwick.github.io/2025/02/19/f...

rrwick.github.io

FASTQ assemblies with Dorado polish

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 20/02/2025

A quick reminder: if CheckM reports an assembly as <100% complete and >0% contaminated, that doesn't necessarily mean it's incomplete or contaminated. Here are RefSeq's CheckM results for a genome I'm confident is 100% complete and 0% contaminated.

RefSeq's CheckM results for GCF_047361035.1, showing 97.99% completeness and 0.39% contamination.

Ryan Wick @rrwick.bsky.social · 19/02/2025

New blog post! Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look: rrwick.github.io/2025/02/19/f...

rrwick.github.io

FASTQ assemblies with Dorado polish

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 07/02/2025

Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here: rrwick.github.io/2025/02/07/d...

rrwick.github.io

Medaka vs Dorado polish

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 20/01/2025

Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets. www.microbiologyresearch.org/content/jour... (1/4)

microbiologyresearch.org

Exploring SNP filtering strategies: the influence of strict vs soft core

Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental ...

Ryan Wick @rrwick.bsky.social · 31/12/2024

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/Autoc... (1/5)

A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

Ryan Wick @rrwick.bsky.social · 17/12/2024

New release of Canu - first one in over 3 years! github.com/marbl/canu/r... The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!

Release Canu v2.3 · marbl/canu

These are release notes for Canu version 2.3, which was released on December 17th, 2024. Canu is specialized for assembly of single-molecule sequences. Full documentation can be found at http://can...

Ryan Wick @rrwick.bsky.social · 17/12/2024

Intrigued by the new dorado polish command! I'm curious how it compares to Medaka's bacterial methylation model, which I've found to be very good.

Ryan Wick @rrwick.bsky.social · 16/12/2024

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

rrwick.github.io

A first look at CycloneSEQ data

a blog for miscellaneous bioinformatics stuff

Ryan Wick @rrwick.bsky.social · 03/12/2024

I've been playing around with LRGE this week and am impressed. It's fast!