George Bouras

Unbelievable, Bakta reached its 1,000th citation!

A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...

...just the entire incredibly supporting binfie community!

Without you, Bakta wouldn't be the same.

Thank you!

Dear community, Bakta needs your help!

To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)

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To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

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

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
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Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...

Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵

📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
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Seems like a reasonable assumption - @jimshaw.bsky.social @rrwick.bsky.social way more expert than me here

Will also say somewhat spookily Ryan just posted an update to this benchmark rrwick.github.io/2025/09/23/a...

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 😄

autocycler (and this benchmark) is for isolates, so I would be cautious extrapolating any results to metagenomes

Box and whisker plot of various assemblers and their number of errors per assembly. Autocycler outperforms all assemblers with the lowest median of <=10 errors per genome

Automated, almost-error-free consensus #assemblies with Autocycler

Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome

Once again, incredible, landmark work from @rrwick.bsky.social

doi.org/10.1093/bioi...

Tool here: github.com/rrwick/Autoc...

#bioinformatics #genomics

GPU-accelerated homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

MVIF 42 program

It's Monday!
...and a new #MVIF program is out! 🤩

Free registration: cassyni.com/s/mvif-42

⭐️ Highlights:
🇦🇺 @gbouras13.bsky.social
🇺🇸 Danica Schmidtke

⭐️ Keynote:
🇺🇸 Peter Turnbaugh

⭐️ Talks:
🇸🇬 Minghao Chia
🇺🇸 @arzamasovalex.bsky.social ‪
🇳🇿 Brooke Wilson

GPU-accelerated homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure prediction, and structural searches with Foldseek.

GPU-accelerated homology search with MMseqs2 | Nature Methods https://www.nature.com/articles/s41592-025-02819-8

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...

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 https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1

De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

www.nature.com/articles/s41...

#microsky #genomics #phagesky #phage defense

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Reprogramming resistance: phage-antibiotic synergy targets efflux systems in ESKAPEE pathogens | mBio Antimicrobial resistance (AMR) is one of the greatest threats to global health. If unaddressed, it is projected to cause over 39 million cumulative deaths globally by 2050 (1). While resistance is a b...

🚨New Review Out🚨
We explore how phage-antibiotic synergy can dismantle efflux-driven resistance in multidrug-resistant ESKAPEE pathogens. By reprogramming bacterial defences, phages offer a precision strategy to restore antibiotic efficacy.

journals.asm.org/doi/10.1128/...

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...

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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Check out Ryan's new blogpost, especially if you work on and polish small eukaryotic genome assemblies - it's always nice when someone adds new features for your tools

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...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...

Preprint: De-novo design of proteins that inhibit bacterial defenses

Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications

Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵

VoM is great for that I'd say (especially the parts of the conference that don't focus on therapy) - would highly recommend that conference. There's also the phage bites online symposium over an arvo run a few times a year by the ASM phage SIG - would recommend that as well

Australian Bioinformatics And Computational Biology Society The Australian Bioinformatics And Computational Biology Society (ABACBS, pron. ˈabəkəs) is the peak body and national scientific and professional society for bioinformatics and computational biology.

Hey mate - that conference I have never heard of (looks a bit predatory tbh). There are no annual phage conferences I know of - you are a year late the international Viruses of Microbes was in Cairns last year (Prague next yr) - I would recommend ABACBS in Adelaide in November though! www.abacbs.org

Examples of protein annotations across functional classification schemes. Yellow: hierarchical classification schemes, red: orthologous/homologous groups, and blue: methods using protein domain information. Protein structures were generated using the ColabFold Alphafold MMseqs2 interactive notebook (version 1.5.2) (57) and visualized using ChimeraX (58). (A) Functional labels associated with the glycogen synthase protein in Escherichia coli (UniprotKB P0A6U8). (B) Functional labels associated with Kehishuvirus sp. tikala major capsid protein (NCBI WEU69752.1).

New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes

by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob

#phagesky #microsky

journals.asm.org/doi/epub/10....

Computational function prediction of bacteria and phage proteins | Microbiology and Molecular Biology Reviews SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advance...

Thrilled to share our new review just published in Microbiology and Molecular Biology Reviews (@asm.org #MMBR):
“Computational Function Prediction of Bacteria and Phage Proteins”
with @gbouras13.bsky.social @linsalrob.bsky.social @bedutilh.bsky.social
🔗 journals.asm.org/doi/10.1128/...

🚨New paper 🚨

Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
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