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Benchmark update: metaMDBG and Myloasm

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Reposted by George Bouras

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 😄

GPU-accelerated homology search with MMseqs2 - Nature Methods

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George Bouras @gbouras13.bsky.social · 15d

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

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Reposted by George Bouras

Ben Vezina @bananabenana.bsky.social · 16d

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

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

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Reposted by George Bouras

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17d

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

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

GPU-accelerated homology search with MMseqs2 - Nature Methods

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Reposted by George Bouras

Microbiome Virtual International Forum @microbiomevif.bsky.social · 16d

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

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Reposted by George Bouras

Tominaga K. (tomiken) @pacyc184.bsky.social · 20d

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

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.

agtools: a software framework to manipulate assembly graphs

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Reposted by George Bouras

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

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 George Bouras

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21d

agtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1

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Reposted by George Bouras

Emmanuele Severi @emmseveri.bsky.social · 23d

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

#microsky #genomics #phagesky #phage defense

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.

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

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Reposted by George Bouras

Zamin Iqbal @zaminiqbal.bsky.social · 28d

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...

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Reprogramming resistance: phage-antibiotic synergy targets efflux systems in ESKAPEE pathogens | mBio

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Reposted by George Bouras

Anita Tarasenko @anitatarasenko.bsky.social · 29d

🚨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/...

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...

journals.asm.org

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Reposted by George Bouras

Zamin Iqbal @zaminiqbal.bsky.social · Sep 7

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...

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...

www.biorxiv.org

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Reposted by George Bouras

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

1 / N

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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George Bouras @gbouras13.bsky.social · Sep 5

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

Ryan Wick @rrwick.bsky.social · Sep 4

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...

Cross-sample homopolymer polishing with Pypolca

Cross-sample homopolymer polishing with Pypolca

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Reposted by George Bouras

Ryan Wick @rrwick.bsky.social · Sep 4

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...