Ben J Woodcroft

Wanted it to be easier to understand so went with linear. Here's what it looks like fwiw - lot easier to fit a straight line..

graph showing number of each community profiling type (amplicon, shotgun-nanopore and shotgun-illumina). Amplicon and shotgun-illumina are in the millions of runs, while shotgun-nanopore is in the tens of thousands of runs.

There was a 34% increase in shotgun metagenomes in 2025 vs 2024 (64% increase for nanopore, now ~15,000), but amplicons are still king.

trophy backlit by coloured lights

Researcher of the year slide

A lucky year in 2025, and now I've a QUT Faculty of Health Researcher of the Year to prove it. Thank you to the many non-myself people who made it happen.

singlem/singlem/appraisal_result.py at d416d391aea9c769d050426ea793121d7deaedb2 · wwood/singlem Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes - wwood/singlem

indeed. It actually just uses the Dark2 palette plus white at the moment. github.com/wwood/single... - should be easy enough to limit the number of colours, but expanding beyond that is hard. What is your use-case here?

@aroneys.bsky.social is this relatively trivial you think? @alexjaf.bsky.social is it simply the number to colour?

Celebrating Excellence at the Centre for Microbiome Research!

We’re thrilled to share that Gene Tyson, @benjwoodcroft.bsky.social and @luispedrocoelho.bsky.social have once again been named Highly Cited Researchers for 2025 by Clarivate!

#HighlyCited2025

GlobDB: a comprehensive species-dereplicated microbial genome resource AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠

Thanks @aroneys.bsky.social @rossenzhao.bsky.social l Raphael Eisenhofer @thepatientwait.bsky.social @daanspeth.bsky.social @Anna-MarieSeelen @ilnamkang.bsky.social @luigallucci.bsky.social and others

SingleM v0.20.2 - ONT/PacBio input reads now supported (if somewhat inefficiently), plus improved Lyrebird database for phage profiling.

Microbial fraction is now prokaryotic fraction, easier to specify input genomes.

Excellent work from @aroneys.bsky.social here. Free to read version at rdcu.be/ePJp4

Public MAG datasets not available at NCBI or ENA Some metagenome assembled genome (MAG) datasets are not available in the standard locations (NCBI / ENA / etc) for a variety of reasons. Here you can contribute new ones you come across. To be recorde...

In the meantime, we've been collecting a list of these at tinyurl.com/mag-collecti.... Feel free to add more you find.

See also GlobDB from @daanspeth.bsky.social which incorporates some of these into a new MAG collection arxiv.org/abs/2506.11896

Yes normal behaviour. See wwood.github.io/singlem/FAQ for the formula - most windows are 60bp, and so if your reads are uniform length you get that.

But you are looking at the OTU table there, perhaps you want the taxonomic profile output (which is a more final output)?

Trimmed reads are bad news when they become short, but if they remain 100bp+ then you should be fine I reckon.
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wwood/singlem Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes - wwood/singlem

Thanks - strange that your Lyrebird experience wasn't good. Please report errors (what did you you?) at github.com/wwood/single... or just via email. We test installation inclusive of DB download at github.com/wwood/single...

But a new version of the lyrebird DB incoming btw.
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the treasure trove of all sequencing datasets

Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...

Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/

Thanks for kind words. By UCEs you mean e.g. 16S? It actually does this already, and tests pass. But it isn't the most efficient and code is a bit crusty and db is out of date, since it doesn't get used much. See wwood.github.io/singlem/FAQ

singlem-benchmarking/bin at main · wwood/singlem-benchmarking Contribute to wwood/singlem-benchmarking development by creating an account on GitHub.

This is great @titus.idyll.org (though to be picky it's SingleM or singlem, not singleM). We wrote a few parsers for other formats at github.com/wwood/single... - it'd be nice if not everyone needed to reinvent (and use standard names for things like coverage inclusive vs exclusive of children).

I wonder if AI could do a good job of that integration. I'd love to learn some Haskell actually, just need to find the time..

Nanopore by thepatientwait · Pull Request #208 · wwood/singlem Working Nanopore build. Important changes: DIAMOND prefilter Uses --range-culling + related args for DIAMOND. These results are now streamed to help memory. Sequences are indexed using gene names ...

There is also a branch that takes nanopore reads as input, which works reasonably well. We are putting some final code touches on it, but maybe helpful - github.com/wwood/single...

Good good, or could be better?

Good q. Imagine that new Chem nanopore should be fine. You can check by running the supplemented package on your genomes and making sure there is the expected number of markers detected. Should be in line with mag completeness.

cheers Daan - here's a thread explaining some of the deets bsky.app/profile/benj...

Thanks for spreading the word @jcamthrash.bsky.social - there's a explanatory thread at bsky.app/profile/benj...

Thanks for considering it for publication. There's a explanation thread at bsky.app/profile/benj...

Much appreciated @bcoltman.bsky.social

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper Nature Biotechnology - Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.

Thanks for reading this thread - share link at rdcu.be/ewqLW

Thanks also to the reviewers including Alice McHardy - very fair and helpful we thought.

Many many to thank, particularly
@aroneys.bsky.social @rossenzhao.bsky.social Mitchell Cunningham, Linda Blackall, Gene Tyson, @cmrqut.bsky.social and dozens of people who have helped with the software, ms, and everyone who tolerated my enthusiasm.

SingleM is BYO genome, you can add your MAGs to the refDB to get profiles which include both known species and your novel MAGs. wwood.github.io/singlem/tool...

Novel lineage detection + 700k profiles makes it possible to recover novel MAGs from taxons you care about. We recovered new genera from the underrepresented Muirbacteria, Wallbacteria, Riflebacteria and Fusobacteria phyla by assembling the right metagenomes.