Antonio Camargo

We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.

academic.oup.com/nar/advance-...

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...

Amazing work! Congratulations, @benjwoodcroft.bsky.social!

Logo for the Sandpiper website

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

@pentamorfico.bsky.social

Scaling laws of bacterial and archaeal plasmids - Nature Communications The capacity of a plasmid to express genes is constrained by parameters such as its length and copy number. Here, Maddamsetti et al. present a computational method that enables rapid and accurate dete...

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

I came across their work by chance too but never really checked out the library. I'm building a Python library for internal use and evaluating backends. I'll probably go with Needletail because PyO3 makes things really easy

Interesting. Did you found it to be substantially faster than needletail?

HMMER. It's everywhere in bioinformatics, not particularly fast, and its development was recently put on hold. It's kind of wild that we still don't have a solid alternative for HMM-to-protein alignment or searching.

Amazing work! I'm looking forward to more articles like these!

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.

Oddly relatable

Today's sequence data infrastructure is set up for failure in the age of AI. Building an open and collaborative sequence platform for both Human and AI scientists.

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.

Admixture’s impact on Brazilian population evolution and health Brazil, the largest Latin American country, is underrepresented in genomic research despite boasting the world’s largest recently admixed population. In this study, we generated 2723 high-coverage who...

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

Bakta Web – rapid and standardized genome annotation on scalable infrastructures Abstract. The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensiv

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)

Clarification about rescued circular contigs · Issue #6 · GaetanBenoitDev/metaMDBG Thanks for the work in MetaMDBG! In the README you mention that the _rc suffix flags "rescued circular " contigs and that the circularity of such sequences is not as reliable. However, I couldn't f...

For example, it seems that the issue that I opened was fixed: github.com/GaetanBenoit...

I don't think so. It was the only assembler that generated clearly wrong assemblies. That said, it may have improved since then

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 😉

My own experience lines up with what the pre-print quantified. I’ve seen a lot of concatemers in my MetaMDBG assemblies

Growth of public metagenomes over time

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.

Nice work! But I think the link you shared is broken, @milja001.bsky.social.

millardlab.org/home/bacteri...