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Antonio Camargo

@apcamargo.bsky.social
814 followers 136 following 65 posts
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Antonio Camargo @apcamargo.bsky.social · 16/08/2026
Obsidian is good, but has no free syncing (although there are alternative things you could use, like git). The most popular option is probably Notion
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Antonio Camargo @apcamargo.bsky.social · 15/04/2026
It’s that wonderful time of year again. A new GTDB release is out :)
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Antonio Camargo @apcamargo.bsky.social · 14/04/2026
Congratulations, @sdeorowicz.bsky.social!
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Sebastian Deorowicz @sdeorowicz.bsky.social · 14/04/2026
10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration www.nature.com/articles/s41...
nature.com
Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology
FAMSA2 accurately aligns millions of protein sequences at high speed.
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Antonio Camargo @apcamargo.bsky.social · 03/04/2026
It doesn't really test the codes explicitly. It tests several gene models (some of which use alternative genetic codes) and picks the best one. If you are looking for new genetic codes, this won't work
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Antonio Camargo @apcamargo.bsky.social · 13/03/2026
It was a while ago, so I don't really remember the reasons. It could have been that I wanted something very specific... I do recall that I could not find a clear reference. Sorry for the bad feedback :/ Again, I'm not super skilled in Rust, so maybe it was something that you would consider trivial.
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Antonio Camargo @apcamargo.bsky.social · 13/03/2026
I tried to integrate it into a package a while ago, but my impression is that you didn't design it to be used as a library (could just be me being terrible in Rust), so I ended up dropping the idea
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Antonio Camargo @apcamargo.bsky.social · 13/03/2026
For conjugation. I recommend CONJscan. For replication initiators, it's more complicated. You can try MOB-Typer (but it is a bit tough to get working) or annotating finding the replication initiator with Pfams and then looking into the closest homologs. I'm not aware of an easy to run pipeline :/
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Antonio Camargo @apcamargo.bsky.social · 13/03/2026
We've been looking into ways to build a more encompassing classification system. As @titus.idyll.org mentioned, there's so much HGT that the assumptions that we use for bacterial taxonomy don't make sense anymore. But there might be a way to find a meaningful pattern within the HGT web :)
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Antonio Camargo @apcamargo.bsky.social · 13/03/2026
I'd say that the best thing you can do at the moment is characterize environmental plasmids according to their conjugation system and replication initiator family.
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Antonio Camargo @apcamargo.bsky.social · 13/03/2026
That's a good question. Right now, I believe COPLA is the best "taxonomy-like" thing that we have. But the software is tough to run and the database is biased towards plasmids from cultivated bacteria (which is unavoidable)
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Simon Roux @simrouxvirus.bsky.social · 03/12/2025
🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...
academic.oup.com
Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st
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Antonio Camargo @apcamargo.bsky.social · 01/12/2025
This looks really good! Congratulations!
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Michael Kuhn @biocs.bsky.social · 15/08/2025
We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky
metalog.embl.de
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
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Axel Visel @axelvisel.bsky.social · 18/11/2025
Soils contain an amazing diversity of functions encoded in plasmids. The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples. Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov www.nature.com/articles/s41...
A stylized infographic showing the workflow for building a global soil plasmidome resource on the left and a textured world map on the right. The workflow depicts three input data streams from metagenomic datasets and isolate plasmids, which pass through steps like quality control, clustering, functional annotation, CRISPR analysis, host assignment, and detection of gene categories such as biosynthetic clusters, antimicrobial resistance, antimicrobial peptides, and CAZymes. All outputs feed into a central SQL database. The world map shows sample locations across the globe as teal circles of varying size, highlighting regions from many plasmids were recovered. Adapted from Fig 1A and 1B in Fiamenghi et al., doi:10.1038/s41467-025-65102-6
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Antonio Camargo @apcamargo.bsky.social · 08/11/2025
That's nice to hear :) Feel free to provide any feedback
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Antonio Camargo @apcamargo.bsky.social · 07/11/2025
Thanks, @acritschristoph.bsky.social!
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
@yishay.bsky.social @jimshaw.bsky.social @simrouxvirus.bsky.social @jgi.doe.gov @berkeleylab.lbl.gov
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
This project came together thanks to many amazing people (see tweet below for handles). A special thanks to Stephen Nayfach, who kicked off UHGV and helped guide it all the way through.
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
To facilitate adoption by the community, we provide online tools to allow users to explore UHGV in the browser. If you don't mind using the command line, we also provide all of the data for download :) 🌐 uhgv.jgi.doe.gov (8/8)
uhgv.jgi.doe.gov
UHGV
A comprehensive resource of viruses from the human gut microbiome that includes thoroughly annotated genomes, protein structures, and a novel hierarchical classification system that systematically org...
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
Taking advantage of the genomic diversity in UHGV, we used comparative genomics to examine in detail diversity-generating retroelements, methyltransferases, and endolysins, proposing mechanisms by which these functions enhance a phage’s capacity to infect new hosts. (7/8)
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
We then examined the genetic factors underlying broader host range and found that functions involved in phage-host interactions across multiple stages of the infection cycle shape a phage's ability to switch hosts. (6/8)
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
Using UHGV, we profiled thousands of human gut metagenomes and identified a subset of hyperprevalent phages found around the globe. Leveraging host prediction data, we found that these phages have markedly higher host ranges. (5/8)
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
Another key challenge in virome research is that most viruses lack taxonomic classification, leading to ad hoc approaches that hinder cross-study comparisons. To address this, we developed a taxonomy-like framework and a tool for assigning user's genomes to UHGV clusters. (4/8)
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
Viral proteins are difficult to annotate, making it hard to infer their biology from genomes. We developed a pipeline that integrates sequence- and structure-based methods to improve functional annotation and reveal novel protein domains. (3/8)
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
The Unified Human Gastrointestinal Virome (UHGV) includes 873,994 viral genomes recovered from the microbiomes of globally diverse populations. Its scale and genome quality make UHGV a valuable reference for future studies of human gut viromes worldwide. (2/8)
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...
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Antonio Camargo @apcamargo.bsky.social · 03/11/2025
The old internet was a better place
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Yunha Hwang @microyunha.bsky.social · 28/10/2025
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.
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ace-gtdb.bsky.social @ace-gtdb.bsky.social · 22/10/2025
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-...
academic.oup.com
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
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Antonio Camargo @apcamargo.bsky.social · 06/09/2025
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...
blast.ncbi.nlm.nih.gov
2025 BLAST NEWS — BlastNews 0.1.1 documentation
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Rayan Chikhi @rayanchikhi.bsky.social · 03/09/2025
🌎👩‍🔬 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...
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Antonio Camargo @apcamargo.bsky.social · 17/07/2025
Amazing work! Congratulations, @benjwoodcroft.bsky.social!
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Ben J Woodcroft @benjwoodcroft.bsky.social · 16/07/2025
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 🧵
Logo for the Sandpiper website
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 02/07/2025
Preprint alert from the group 🚨 super fast grep-like sequence selection
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Antonio Camargo @apcamargo.bsky.social · 02/07/2025
@pentamorfico.bsky.social
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Cameron Thrash @jcamthrash.bsky.social · 02/07/2025
Scaling laws of bacterial and archaeal plasmids www.nature.com/articles/s41... #jcampubs
nature.com
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...
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Antonio Camargo @apcamargo.bsky.social · 25/06/2025
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
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Antonio Camargo @apcamargo.bsky.social · 25/06/2025
Interesting. Did you found it to be substantially faster than needletail?
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Antonio Camargo @apcamargo.bsky.social · 21/06/2025
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.
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Antonio Camargo @apcamargo.bsky.social · 15/06/2025
Amazing work! I'm looking forward to more articles like these!
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Robert Aboukhalil @robert.bio · 10/06/2025
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!
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Simon Roux @simrouxvirus.bsky.social · 13/06/2025
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...
doi.org
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Sebastian Schmidt @tsbschm.bsky.social · 03/06/2025
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.
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Antonio Camargo @apcamargo.bsky.social · 03/06/2025
Oddly relatable
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Yunha Hwang @microyunha.bsky.social · 02/06/2025
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:
tattabio.substack.com
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.
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Jim Shaw @jimshaw.bsky.social · 28/05/2025
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
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
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Tábita Hünemeier @hunemeier.bsky.social · 15/05/2025
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.
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Eduardo Amorim @cegamorim.bsky.social · 15/05/2025
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 👏
science.org
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...
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STCmicrobeblog @stcmicrobeblog.bsky.social · 28/04/2025
schaechter.asmblog.org/schaechter/2... #MicroSky #Archaea #ArchaeaSky #SymbioSky
schaechter.asmblog.org
Cultivating the Ancestors (4|4)
by Christoph — Having one or two 'Asgard' archaea under the microscope – after having cultivated them with great effort and even more patience – and looking them in the face is exciting, but a bit uns...
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