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Ryan Wick @rrwick.bsky.social · 9d

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...
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Ryan Wick @rrwick.bsky.social · 9d

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.
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Ryan Wick @rrwick.bsky.social · 9d

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

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Ryan Wick @rrwick.bsky.social · 14d

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 · 14d

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 · 14d

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 · 15d

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 · 15d

Boxplots showing the benchmarking results from my blog post: old-vs-new versions of metaMDBG and Myloasm

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Ryan Wick @rrwick.bsky.social · 15d

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 😄

Benchmark update: metaMDBG and Myloasm

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

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Reposted by Ryan Wick

Vijini Mallawaarachchi @vijinim.bsky.social · 21d

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...

www.biorxiv.org

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Reposted by Ryan Wick

Jim Shaw @jimshaw.bsky.social · Sep 7

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

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

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

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Ryan Wick @rrwick.bsky.social · Sep 7

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

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Ryan Wick @rrwick.bsky.social · Sep 7

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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