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Ryan Wick @rrwick.bsky.social · 30/07/2026

Yes, doubled plasmids would contribute to extra bases. Also, Flye sometimes makes an extra contig for repetitive sequences. E.g. there will be some repeat in the chromosome that's correctly assembled in the chromosome, but then Flye will also make a separate contig for that repeat.

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Ryan Wick @rrwick.bsky.social · 30/07/2026

I suspect it’s a combination of missing plasmids and extra contigs. If an assembly contains an extra 1 kbp contig (e.g. redundant sequence from the genome), that counts as 1000 errors. It’s a very unforgiving metric!

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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.com

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

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

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

I just reread the "Assembler summaries" section, and it holds up okay. But Myloasm and metaMDBG are missing, since they weren't around back then. I sometimes consider a sequel to that paper, where I do something similar with modern ONT reads...

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

Notable finding #2: The new autocycler_fast.sh pipeline did just as well as its bigger/slower sibling. If you've been avoiding Autocycler because of the computational time, this might be worth a look: github.com/rrwick/Autoc... (3/3)

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

Notable finding #1: the current version of metaMDBG is quite good! Fast, very memory efficient and now one of the most accurate assemblers. Nice work, @gaetanbenoit.bsky.social! github.com/GaetanBenoit... (2/3)

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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

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

I also put a small update on my blog post explaining this: rrwick.github.io/2026/06/19/d...

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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...

biorxiv.org

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,...

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

What custom-tuned basecalling model are you using? Something trained in-house? Regarding whether Dorado polish would help or make things worse, the best check would be to do some Illumina sequencing as well.

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

Sorry for the slow reply - just saw this! I don't have much experience with archaea, but I have no reason to expect ONT would perform poorly. If your samples contain unique DNA modifications, that might result in lower assembly accuracy, since those mods probably aren't in their training set.

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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

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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

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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

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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

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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...

biorxiv.org

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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...

medrxiv.org

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...

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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

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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 ...

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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

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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

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

And since both metaMDBG and Myloasm had new versions after the paper was accepted, here's a blog post with an updated benchmark: rrwick.github.io/2025/09/23/a... (3/3)

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

Here's the ultra-short version: If you want the best possible long-read bacterial genome assemblies, Autocycler is the tool for you! It is computationally intensive (due to the need to generate many alternative input assemblies) but consistently more accurate than other methods. (2/3)

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Ryan Wick @rrwick.bsky.social · 24/09/2025

One caveat though: my experience is with isolates that (usually) have a single 'true' sequence to aim for. In a metagenome with natural variation (i.e. a mixture of multiple 'true' sequences), I'm not sure how Dorado/Medaka would behave...

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

I have limited experience with long-read metagenome assembly, so I don't have any special insight here. But I like the examples shown @floriantrigodet.bsky.social's preprint - it shows how sometimes one strange read (e.g. a chimera) can throw off the assembly.

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

No, the assemblies are not Dorado/Medaka polished. I predict doing so would significantly reduce error rates, especially for the higher-error assemblies - Dorado/Medaka is quite good at fixing small-to-medium scale errors. But for lower-error assemblies (e.g. Autocycler), it may not change much.

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

I agree, most real-world MAGs probably have more errors than isolates, especially if low depth. Also, metagenomes may have within-species variation, and then the ideal MAG is (arguably) some sort of consensus. Especially if there is structural variation, this can be a BIG challenge for assemblers.

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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

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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

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Ryan Wick @rrwick.bsky.social · 07/09/2025

Amazing, thanks! Will keep an eye out for this preprint.

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Ryan Wick @rrwick.bsky.social · 07/09/2025

I haven't yet, but that is absolutely something I should try. I should also more generally educate myself on best practices in telomere assembly, e.g. with that paper Adam linked. This is new to me!

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Ryan Wick @rrwick.bsky.social · 05/09/2025

Thanks for this - looks interesting! In the paper you said: "...Illumina sequencing can generate spurious indels within HTs, especially for HT lengths longer than 14 bp." Do you have a sense of how bad this gets for really long homopolymers, e.g. 20+ bp?

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Ryan Wick @rrwick.bsky.social · 05/09/2025

I'm sure there are more robust ways to go about telomere assembly - I'm not very experienced with T2T eukaryote genome assemblies 😬

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Ryan Wick @rrwick.bsky.social · 05/09/2025

And my manual telomere fixing was makeshift. I pieced together a few assemblies (mostly from Flye) that extended all the way to the telomeres. And then I manually repaired the telomeres to be exact 6-mer repeats - i.e. I assumed any deviation from the 6-mer was ONT error not real biology.

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Ryan Wick @rrwick.bsky.social · 05/09/2025

Since all Illumina sequencing involves some PCR (bridge amplification), I also wonder at what length Illumina reads start to fail with homopolymers. Can they reliably sequence 20-mers? 40-mers? 60-mers? It's a hard question to answer if every sequencing tech struggles with these...

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Ryan Wick @rrwick.bsky.social · 05/09/2025

I too am wary. I suppose the hope is that by limiting changes to long homopolymers, polishing will fix more errors than it introduces. I.e. I'm guessing that ONT's long-homopolymer error rate is greater than cross-sample homopolymer differences. But this is very much unproven!

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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

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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...

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

However, I hear rumours that ONT might be working on a new move-table-aware bacterial polishing model. See my blog post from Feb for details: rrwick.github.io/2025/02/07/d.... If true, I'll be eager to test it out when released.

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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.

github.com

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...

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Ryan Wick @rrwick.bsky.social · 30/05/2025

Good to know - thanks for clarifying. Makes sense for a tool that's designed to work with big metagenomic datasets. I'm using it a bit out of its domain on a bacterial isolate.

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Ryan Wick @rrwick.bsky.social · 30/05/2025

The read set was only 240 MB (gzipped), so it is memory hungry. The myloasm docs do acknowledge that it uses more memory than other assemblers. Also, I ran my tests on an ARM Mac, but the docs suggest that myloasm (specifically the polishing step) will be even faster on x86-64 CPUs with AVX2.

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Ryan Wick @rrwick.bsky.social · 30/05/2025

Just ran a few more tests through GNU time: 1 thread: 435 seconds, 10.1 GB RAM 2 threads: 238 seconds, 10.0 GB RAM 4 threads: 133 seconds, 10.1 GB RAM 8 threads: 73 seconds, 10.1 GB RAM 16 threads: 49 seconds, 13.3 GB RAM

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

I tested myloasm on a 50x Klebsiella isolate, and it was very fast - only took about 1 minute to complete (on my Macbook).

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

Even though it's designed for metagenomes, I suspect it might work nicely on bacterial isolates as well, especially if you filter out low-depth contigs. This is what I've found for metaMDBG, a long-read metagenome assembler from @gaetanbenoit.bsky.social.

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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.

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