gbouras13.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Unicore is now published on GBE 🚀 Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n 📃 doi.org/10.1093/gbe/evaf109

submitted 22 hours ago • 3 comments

Promising toolkit for binning and visualizing assembly graphs. The assembly graph is an underutilized source of binning information IMO gbintk.readthedocs.io/en/latest/

submitted 5 days ago • 1 comment

Journal of Open Source Software: GraphBin-Tk: assembly graph-based metagenomic binning toolkit https://joss.theoj.org/papers/10.21105/joss.07713

submitted 5 days ago • 0 comments

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

submitted 6 days ago • 5 comments

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

submitted 7 days ago • 4 comments

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...

submitted 13 days ago • 2 comments

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

submitted 14 days ago • 1 comment

Amira: gene-space de Bruijn graphs to improve the detection of AMR genes from bacterial long reads https://www.biorxiv.org/content/10.1101/2025.05.16.654303v1

submitted 16 days ago • 0 comments

Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social

submitted 15 days ago • 0 comments

We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments. 🌐 afesm.foldseek.com Read more about the work in the skeetorial 🦋 bsky.app/profile/mart... or our preprint 📄 www.biorxiv.org/content/10.1...

submitted 19 days ago • 2 comments

www.biorxiv.org/content/10.1... Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use) github.com/rrwick/Autoc...

submitted 19 days ago • 2 comments

Introducing our invited speaker for the session on 'Viral Dark Matter' we have Rachel Seongeun Kim from the Seoul National University!!!! The registrations for on-site & remote participation are still open! More info: RdRp.io #RdRpSummit2025

submitted 32 days ago • 1 comment

We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue doi.org/10.1093/nar/... Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI: bakta.computational.bio (1/5)

submitted 36 days ago • 1 comment

The sequence analysis session of #RECOMB2025 is off to a great start with @jimshaw.bsky.social presenting devider, a new algorithm for haplotyping small sequences from long-read sequencing. www.biorxiv.org/content/10.1...

submitted 38 days ago • 1 comment

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...

submitted 38 days ago • 4 comments

Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology www.nature.com/articles/s41...

submitted 62 days ago • 7 comments

Big Fantastic Virus Database (BFVD) version 2 improves 31% of predictions through 12 ColabFold recycles. PAEs and MSAs now also available for download and in the webserver. 🌐https://bfvd.foldseek.com 💾https://bfvd.steineggerlab.workers.dev/ 1/3

submitted 65 days ago • 2 comments

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them? If so, you might this little project: github.com/rrwick/conda...

submitted 69 days ago • 1 comment

A question while writing up a study proposal: What are characters of a good prokaryotic gene alignment? The way I learned it from no-one is a good alignment gives well-scoring inferred tree later, but that feels a bit iffy and takes too long to confirm. Any great articles/insights on this? 🦠🧫🧬💻

submitted 78 days ago • 1 comment

Check out this list of awesome #virome tools and be sure to add yours! github.com/shandley/awe... #phagesky #microsky

submitted 83 days ago • 0 comments

Metabuli App preprint is out! 💻Taxonomic classification & interactive visualization—right on your laptop 🛠️Create new databases or update existing ones with new sequences. 🧵1/5 github.com/steineggerla... www.biorxiv.org/content/10.1101/2025.03.10.642298v1

submitted 82 days ago • 1 comment

ChimeraX can run Foldseek to find similar structures, such as distantly related homologs, and analyze the results, for example, mapping all ligands onto your query structure. Here are ligands mapped onto Nipah virus G protein. www.rbvi.ucsf.edu/chimerax/dat...

submitted 89 days ago • 2 comments

🦠🧬🖥️ New Bakta DB v6.0 released! After a year, it was time for a Bakta database update - and it's a huge one: - IPS: 330.9M - PSC: 135.3M - PSCC: 37M doi.org/10.5281/zeno... 👇 1/6

submitted 89 days ago • 1 comment

New preprint is out! We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling. Read it here: www.biorxiv.org/content/10.1... Data & code: github.com/rrwick/Are-r... (1/8)

submitted 93 days ago • 2 comments

"benchmarking multiple assembly and variant-calling pipelines....read-based methods consistently achieved high accuracy. Assembly-based approaches performed well in some cases but were highly dependent on assembly quality" www.biorxiv.org/content/10.1... from Ryan Wick&co

submitted 95 days ago • 0 comments

Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...

submitted 98 days ago • 3 comments

A quick reminder: if CheckM reports an assembly as <100% complete and >0% contaminated, that doesn't necessarily mean it's incomplete or contaminated. Here are RefSeq's CheckM results for a genome I'm confident is 100% complete and 0% contaminated.

submitted 104 days ago • 6 comments

Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here: rrwick.github.io/2025/02/07/d...

submitted 117 days ago • 2 comments

Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects. 📄 nature.com/articles/s41... 🌐 search.foldseek.com

submitted 117 days ago • 0 comments

Recently we have been doing lots of work on how modern #AI methods can be applied to studying virus evolution, so it felt like great timing to write a perspective about it! Very happy to see our paper as editor's pick in JVI!🥳🥳 doi.org/10.1128/jvi....

submitted 119 days ago • 2 comments

And now with the working link! journals.asm.org/doi/10.1128/...

submitted 124 days ago • 0 comments

I’m excited to share our latest preprint in collaboration with @Halllab.bsky.social In this work, led by PhD student James Docherty, we investigated the presence of #prophages and anti-phage defence systems in human-associated #bifidobacteria: www.biorxiv.org/content/10.1... (1/4)

submitted 132 days ago • 1 comment

New paper alert!! 🚨🚨 And it's on the coolest (and most mysterious 🕵️) group of viruses I've worked on so far! With Sej Modha we uncovered >800 new anellovirus genomes from human metagenomes and looked for clues on these tiny, elusive viruses biology! academic.oup.com/ve/article/1...

submitted 132 days ago • 5 comments

Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets. www.microbiologyresearch.org/content/jour... (1/4)

submitted 134 days ago • 2 comments

Foldseek 10 with 4-27x (1-8 GPUs) faster search through MMseqs2-GPU. Faster ProstT5 protein search w/o structure prediction through multi-GPU/Apple Metal, new BFVD/BFMD databases and multimer clustering (preview). 💾 github.com/steineggerla... 📄 www.biorxiv.org/content/10.1... 🐍 available in bioconda

submitted 134 days ago • 1 comment

New paper out! I'm excited to share our latest work in Bioinformatics Advances! We've developed Sphae, a bioinformatics pipeline to evaluate phage therapeutic potential. doi.org/10.1093/bioa... Try it here: github.com/linsalrob/sp... #PhageTherapy #AMR #Bioinformatics #phagesky

submitted 137 days ago • 0 comments

The Foldseek webserver for fast protein structure searches now features a Sankey tree taxonomy visualization and filter, allowing to subset hits by clades. Developed by my talented student @sunjaelee.bsky.social. Try it out! 🌐 search.foldseek.com

submitted 137 days ago • 4 comments

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)

submitted 154 days ago • 2 comments

1/11 - With Karin Mitosch and Clément Potel + colleagues in Savitski lab and @typaslab.bsky.social @embl.org, I’m very happy to share our discovery of a hyper-promiscuous phage protein kinase (T7K) which broadly deactivates bacterial defenses! 🦠 www.biorxiv.org/content/10.1...

submitted 162 days ago • 1 comment

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n 📄 www.biorxiv.org/content/10.1... 💾 github.com/steineggerla...

submitted 162 days ago • 2 comments

Were you looking for a protein structure database of all animal viruses with: - taxonomy, - protein and - genome coordinate annotations to browse over the holidays? (I know I was!) Viro3D is here!! #viro3d viro3d.cvr.gla.ac.uk

submitted 164 days ago • 3 comments

We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! github.com/bluenote-157... www.biorxiv.org/content/10.1... 1/5

submitted 168 days ago • 1 comment

New release of Canu - first one in over 3 years! github.com/marbl/canu/r... The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!

submitted 168 days ago • 1 comment

“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯 www.statnews.com/sponsor/2024...

submitted 182 days ago • 3 comments

I've been playing around with LRGE this week and am impressed. It's fast!

submitted 183 days ago • 0 comments