A BLAST update adding support for compressed files and csv output with headers is a Good Friday night surprise! blast.ncbi.nlm.nih.gov/doc/blast-ne...

🌎👩‍🔬 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...

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

Preprint alert from the group 🚨 super fast grep-like sequence selection

Scaling laws of bacterial and archaeal plasmids www.nature.com/articles/s41... #jcampubs

Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen... Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

The Koonin Law of Computatoinal Biology: Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.

At Tatta Bio, we have been thinking deeply about the sequence-to-function problem. We believe that before AI can power functional prediction, we first need to rethink how we curate, manage, and share sequence data. Here, we share our initial ideas on what we are building next:

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

Our new paper is out in @science.org! By exploring the rich genetic diversity of Brazil, we show how fine-scale genomic analyses reveal that this diversity, rooted in Indigenous ancestry and centuries of complex demographic history, plays a key role in population health.

Very proud of my colleagues and friends for their amazing publication out in Science today! Nunes et al. "Admixture’s impact on Brazilian population evolution and health" www.science.org/doi/10.1126/... @hunemeier.bsky.social @macscastro.bsky.social 👏

schaechter.asmblog.org/schaechter/2... #MicroSky #Archaea #ArchaeaSky #SymbioSky

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)

Unique investigation of some errors in long read assemblers. In particular these remarkably chimeric contigs are 😱, if rare.... Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉

A 1.0 release for Sandpiper. 700,000 microbial community profiles (3x the last version, 4.7 Pbp metaG), searchable via the @ace-gtdb.bsky.social R226 taxonomy that just dropped. MetaGs are going exponential, but we are still nowhere near a MAG for all species. sandpiper.qut.edu.au #microsky 🧬🖥️ 1/2

GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.

Is the genome just a bag of genes? A new paper in Science now reports that for two thirds of an organisms' genes the position along the chromosome is actually very tightly constrained! Amazing work from my favorite night scientist Martin Lercher and his team! www.science.org/doi/10.1126/...

CoverM is published! CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs

🚨New paper!🚨 A comprehensive take on the origins and evolution of translation factors & how these essential players evolved across the tree of life. 🌍🧬 Led by Evrim Fer @uwmadisonmdtp.bsky.social grad student! 👏 Free access: www.sciencedirect.com/science/arti... @cp-trendsgenetics.bsky.social

The abstract submission & registration for #RdRpSummit2025 is NOW OPEN!!! 🎉🙌 Do you work on RNA virus discovery using RdRps? Are you joining the #ViBioM2025 in Portugal? Consider submitting your research in one of our sessions! More info: RdRp.io

Publishing a paper in Nature while based in Brazil is an incredible achievement. Huge congratulations to the authors! I'm excited to give this a proper read :)

One of the great things about bioinformatics is how open it can be. Contributing to a project you admire can actually get you involved in it :)

I'm very happy to report that Matt Schechter's PhD work is now online as a pre-print: "Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities", www.biorxiv.org/content/10.1... Here's a little 🧵 about it.

This preprint makes a point that is valid for a lot of machine learning approaches. Organisms or genes are linked by evolutionary history; they are not independent. This results in correlation between learning and test sets, and often in over-optimistic evaluations of the methods' outcome.

In Science Advances: "We took a deep dive into over 1.8 million bacterial and archaeal genomes to see how much of their diversity we’ve actually captured. Turns out that despite all the genomes we’ve sequenced, we’ve only scratched the surface." -Dongying Wu 🖥️🧬🦠 biosciences.lbl.gov/2025/01/17/t...

🚨Postdoc position(s) alert🚨 If you like to develop new bioinformatic tools for *human* microbiome analysis, are interested by virus/phages, we (JGI Viral Genomics and Microbiome Data groups) may have a great position for you ! No official job posting yet, but email or DM if you are interested !

We found that many bacterial species use exogenous peptidoglycan fragments - released by lysis of neighboring cells - as a general danger signal, triggering a danger response that protects bacteria against many dangers: biofilm formation. Details here 👇 www.nature.com/articles/s41...

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)

RNA virologists, check out "The protein structurome of Orthornavirae and its dark matter" by Pascal Mutz, Valerian Dolja, Eugene Koonin et al (including @simrouxvirus.bsky.social, @apcamargo.bsky.social, @urineri.bsky.social, @anamarijabutkovic.bsky.social) journals.asm.org/doi/10.1128/...

Don't use red and green data lines/surfaces in the same panel please #chemsky. It can be difficult for some colorblind readers to differentiate them. I've accepted (in principle) 2 papers today, and both sets of authors were asked to remove red/green colour contrasts www.nature.com/articles/d41...

An interesting paper for the EV (extracellular vesicle) fans by Patel et al. @ahnaskop.bsky.social lab: "Extracellular vesicles, including large translating vesicles called midbody remnants, are released during the cell cycle" www.molbiolcell.org/doi/10.1091/...

Can LLM agents discover novel protein functions? Introducing Gaia Agent 🌎 🤖: an AI biologist capable of reasoning across genomic contexts to predict functions of proteins! Gaia Agent is now integrated with Gaia Search at gaia.tatta.bio

If you are at #NeurIPS2024 don't miss @ancornman1.bsky.social's talk on OMG/gLM2 at 9AM! @workshopmlsb.bsky.social East meeting room 11,12

Excited to be at #NeurIPS this week. @ancornman1.bsky.social will give a spotlight talk at the @workshopmlsb.bsky.social on gLM2/OMG! Please reach out if you want to chat about gLM2/OMG/Gaia and our latest projects😇 www.biorxiv.org/content/10.1...

Very cool work from Yang Lu et al. demonstrating miscalibration of BLASTP’s E-values and generating well-calibrated values via a knockoff-based approach (cc @mikelove.bsky.social) - academic.oup.com/bioinformati...! More analyses could benefit from knockoff-based approaches.

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience

Hello 🦋 #protein / #microbio / #BioML community! We are excited to release Gaia🌎, a context-aware protein search tool, extending protein search and discovery capabilities beyond sequence and structure, to include *genomic context*. Search your favorite protein sequences with on gaia.tatta.bio

New GPU-based MMseqs2: 20x faster searches on a single L40S (approx. as fast as a RTX 4090) vs. a 128-core CPU. This work enables to set up a very cost-efficient ColabFold MSA GPU server. 🧵🧵 📄 www.biorxiv.org/content/10.1... 💾 mmseqs.com 🗞️ developer.nvidia.com/blog/boost-a...

The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling From friends at Tatta Bio GitHub: github.com/TattaBio/OMG www.biorxiv.org/content/10.1...

Terrabacteria: redefining bacterial envelope diversity, biogenesis and evolution #NatureRevMicro from Simonetta Gribaldo www.nature.com/articles/s41...

AntiDefenseFinder! And it is available also as an option with DefenseFinder: defensefinder.mdmlab.fr Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements www.biorxiv.org/content/10.1...

Methanogenesis outside the Euryarchaeota experimentally demonstrated by three cultivation-driven studies (two from my lab)! A long🧵.🐻with me tinyurl.com/4v4fkda6 tinyurl.com/yr4p7js6 tinyurl.com/mtsrj6b9

If you are interested in prophages, we have a new database: Prophage-DB. Check it out and all feedback is welcome biorxiv.org/cgi/content/...

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution #ISMEJournal from Gergely Szöllősi and collagues (Phil Hugenholtz, Anja Spang, Cecile Gubry-Rangin, Paul O Sheridan, Laura Eme, Rochelle M Soo and more academic.oup.com/ismej/advanc...

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts - Nature Microbiology www.nature.com/articles/s41... @apcamargo.bsky.social Are these new genomes already in the current version of IMG/VR or would I want to download separately and combine for now?

github.com/rcedgar/usea... USEARCH is... open source now (!)

It's the most wonderful time of the year: the time when we all learn about the latest nanopore updates via screenshots of tweets of photos of slides Looks not disappointing, no sign of the accuracy wall! And dorado 0.7 is now out with the new models: github.com/nanoporetech...

I reviewed the AlphaFold3 paper from DeepMind for the journal Nature. I tried really hard to get the editors to demand that DeepMind release the code (even an executable) so people could do the many high-throughput studies we saw for AF2 (see image from my review). I failed. So just a server 4 now.

If you write a bioinformatics software package intended for others to use: Don't spit out diagnostic messages on the console. Some of that info is better kept in the documentation, the rest in the results object, for programmatic access. If your tool is good, it'll soon be one piece in a tool chain.