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Antonio Camargo @apcamargo.bsky.social · Sep 6

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...

2025 BLAST NEWS — BlastNews 0.1.1 documentation

blast.ncbi.nlm.nih.gov

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Reposted by Antonio Camargo

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 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 · Jul 17

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

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Reposted by Antonio Camargo

Ben J Woodcroft @benjwoodcroft.bsky.social · Jul 16

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 🧵

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Reposted by Antonio Camargo

Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 2

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

Antoine Limasset @npmalfoy.bsky.social · Jul 2

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...

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

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Antonio Camargo @apcamargo.bsky.social · Jul 2

@pentamorfico.bsky.social

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Reposted by Antonio Camargo

Cameron Thrash @jcamthrash.bsky.social · Jul 2

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

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Antonio Camargo @apcamargo.bsky.social · Jun 25

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 · Jun 25

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

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Antonio Camargo @apcamargo.bsky.social · Jun 21

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 · Jun 15

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

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Reposted by Antonio Camargo

Robert Aboukhalil @robert.bio · Jun 10

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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Reposted by Antonio Camargo

Simon Roux @simrouxvirus.bsky.social · Jun 13

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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Reposted by Antonio Camargo

Sebastian Schmidt @tsbschm.bsky.social · Jun 3

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 · Jun 3

Oddly relatable

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Reposted by Antonio Camargo

Yunha Hwang @microyunha.bsky.social · Jun 2

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

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Reposted by Antonio Camargo

Jim Shaw @jimshaw.bsky.social · May 28

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 - metagenomic assembly with (noisy) long reads

myloasm-docs.github.io

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Reposted by Antonio Camargo

Tábita Hünemeier @hunemeier.bsky.social · May 15

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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Reposted by Antonio Camargo

Eduardo Amorim @cegamorim.bsky.social · May 15

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 👏

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

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Reposted by Antonio Camargo

STCmicrobeblog @stcmicrobeblog.bsky.social · Apr 28

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

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Reposted by Antonio Camargo

Oliver Schwengers @oschwengers.bsky.social · Apr 28

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
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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

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Antonio Camargo @apcamargo.bsky.social · Apr 26

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

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...

github.com

Antonio Camargo @apcamargo.bsky.social · Apr 26

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

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Reposted by Antonio Camargo

Alex Crits-Christoph @acritschristoph.bsky.social · Apr 25

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 😉

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Antonio Camargo @apcamargo.bsky.social · Apr 26

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

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