Antonio Camargo
@apcamargo.bsky.social
Reposted by Antonio Camargo
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...
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...
November 18, 2025 at 7:18 PM
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...
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...
🚨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...
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...
November 6, 2025 at 5:26 PM
🚨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...
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...
Reposted by 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.
October 28, 2025 at 1:47 PM
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.
Reposted by Antonio Camargo
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/nar/advance-...
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
academic.oup.com
October 22, 2025 at 2:20 PM
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/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...
blast.ncbi.nlm.nih.gov/doc/blast-ne...
2025 BLAST NEWS — BlastNews 0.1.1 documentation
blast.ncbi.nlm.nih.gov
September 6, 2025 at 4:53 AM
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/doc/blast-ne...
Reposted by Antonio Camargo
🌎👩🔬 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...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 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...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Reposted by Antonio Camargo
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 🧵
July 16, 2025 at 9:59 PM
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 🧵
Reposted by Antonio Camargo
Preprint alert from the group 🚨 super fast grep-like sequence selection
A common approach is to use k-mer indexes to identify datasets that share a significant number of k-mers with a query sequence.
This problem has been studied extensively, and I recommend the survey of @camillemrcht.bsky.social, a great introduction to the subject
genome.cshlp.org/content/31/1...
This problem has been studied extensively, and I recommend the survey of @camillemrcht.bsky.social, a great introduction to the subject
genome.cshlp.org/content/31/1...
Data structures based on k-mers for querying large collections of sequencing data sets
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
July 2, 2025 at 1:38 PM
Preprint alert from the group 🚨 super fast grep-like sequence selection
Reposted by Antonio Camargo
Scaling laws of bacterial and archaeal plasmids www.nature.com/articles/s41... #jcampubs
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...
www.nature.com
July 2, 2025 at 3:34 PM
Scaling laws of bacterial and archaeal plasmids www.nature.com/articles/s41... #jcampubs
Reposted by Antonio Camargo
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!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
June 10, 2025 at 4:27 PM
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!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Reposted by Antonio Camargo
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
June 13, 2025 at 8:22 PM
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...
Reposted by Antonio Camargo
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.
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.
June 3, 2025 at 12:31 PM
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.
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.
Reposted by Antonio Camargo
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:
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.
tattabio.substack.com
June 2, 2025 at 4:23 PM
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:
Reposted by Antonio Camargo
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
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
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
Reposted by Antonio Camargo
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.
May 15, 2025 at 7:46 PM
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.
Reposted by Antonio Camargo
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 👏
Nunes et al. "Admixture’s impact on Brazilian population evolution and health" www.science.org/doi/10.1126/...
@hunemeier.bsky.social @macscastro.bsky.social 👏
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...
www.science.org
May 15, 2025 at 6:04 PM
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 👏
Nunes et al. "Admixture’s impact on Brazilian population evolution and health" www.science.org/doi/10.1126/...
@hunemeier.bsky.social @macscastro.bsky.social 👏
Reposted by Antonio Camargo
Reposted by Antonio Camargo
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)
doi.org/10.1093/nar/...
Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)
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
doi.org
April 28, 2025 at 8:47 AM
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)
doi.org/10.1093/nar/...
Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)
Reposted by Antonio Camargo
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 😉
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 😉
April 25, 2025 at 2:46 PM
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 😉
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 😉
Reposted by Antonio Camargo
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
April 17, 2025 at 11:06 AM
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
Reposted by Antonio Camargo
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.
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 18, 2025 at 7:13 PM
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.
Reposted by Antonio Camargo
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/...
Martin Lercher and his team!
www.science.org/doi/10.1126/...
April 11, 2025 at 5:56 PM
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/...
Martin Lercher and his team!
www.science.org/doi/10.1126/...
Reposted by Antonio Camargo
CoverM is published!
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics
AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r
academic.oup.com
April 9, 2025 at 1:24 PM
CoverM is published!
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
Reposted by Antonio Camargo
🚨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
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
March 24, 2025 at 2:46 PM
🚨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
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
Reposted by Antonio Camargo
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
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
February 19, 2025 at 9:10 PM
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
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