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Austin Richardson

@agdr.org

350 followers 320 following 24 posts

Metagenomicist @onecodex.bsky.social. My cat’s name is Nancy

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Austin Richardson @agdr.org · Dec 13

NCBI's Taxonomy changes over time. We built Taxonomy Time Machine to track these changes:

🕰️ app: taxonomy.onecodex.com
📄 pre-print: www.biorxiv.org/content/10.1...

A screenshot of a webpage titled "Taxonomy Time Machine" showing the taxonomic lineage and descendants of the Influenza A Virus

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Reposted by Austin Richardson

🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 13d

Apple's approach to protein structure is great for accessibility - & potentially biological realism - reasons.

Eg, prediction could be achieved w/ smaller compute & the generative nature of prediction allows for multiple conformations

A summary here: genomely.substack.com/p/simplefold...

SimpleFold and the Future of Protein Folding

A Generative Shift in Protein Folding

genomely.substack.com

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Reposted by Austin Richardson

Paul Medvedev @pashadag.bsky.social · 13d

If you're wondering why we're hosting the pre-print via dropbox, its because arXiv (and bioRxiv) did not accept it (because it is a review). Its a bit disconcerting, because a review is precisely the type of paper that would benefit a lot from pre-publication dissemination and feedback.

Paul Medvedev @pashadag.bsky.social · 13d

Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

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Austin Richardson @agdr.org · 16d

Closed my eyes for a sec and summoned another earthquake

Austin Richardson @agdr.org · 23d

they should invent a type of volatile memory that gets heavier the more data it contains

Reposted by Austin Richardson

Bede Constantinides @bedec.bsky.social · 26d

Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...

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Austin Richardson @agdr.org · Aug 31

NCBI BLAST can now output a proper CSV with headers 👏🎉: www.ncbi.nlm.nih.gov/books/NBK131...

BLAST+ Release Notes

Note: If building BLAST+ from source code, the Zlib, Zstandard and Bzip2 libraries will be needed.

www.ncbi.nlm.nih.gov

Austin Richardson @agdr.org · Aug 25

you can just pour milk over trail mix and eat it like cereal

Austin Richardson @agdr.org · Aug 18

"You are standing in an open field west of a white house, with a boarded front door."

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Reposted by Austin Richardson

Ragnar {Groot Koerkamp} @curiouscoding.nl · Aug 6

Little writeup on the speed of fasta parsers, at last.

Basically: both needletail and paraseq are process input linearly, and thus have a limit around 4 GB/s.

By giving each thread its own slice of the input file, we're limited by RAM bandwidth instead :)

curiouscoding.nl/posts/fasta-...

With 3 threads, the middle thread processes the reads starting in the middle third of the fasta file.

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Reposted by Austin Richardson

Dr. Stephanie @punkrockscience.bsky.social · Jul 23

I do not enjoy that we now live in a world where seeing this banner at the top of PubMed makes me nervous.

Red banner from the top of PubMed, saying "Service Alert: Planned Maintenance beginning July 25th. Most services will be unavailable for 24+ hours starting 9pm EDT. Learn more about the maintenance."

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Reposted by Austin Richardson

Alex Crits-Christoph @acritschristoph.bsky.social · Jul 22

TIL the EBV genome is *included in the hg38 assembly* so that EBV reads are not erroneously mapped elsewhere to the human genome. That's certainly .... an interesting solution ... 🤯

But it enabled this extremely cool work:

Caleb Lareau @caleblareau.bsky.social · Jul 22

In a cool twist of fate, the EBV contig is in hg38 to mop up unscrupulous EBV reads, a by-product of immortalizing lymphoblastic cell lines (used in 1000 Genomes Project, etc.). Hence, a simple `samtools view` could get a measure of persistent EBV DNA in large WGS cohorts, e.g., UK Biobank. 4/

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Reposted by Austin Richardson

Philipp Bayer @philippbayer.bsky.social · Jul 21

This is a bad take
stevensalzberg.substack.com/p/i-know-gen...

Saying that DNA data is like your browsing data and can can therefore be leaked is a false equivalence. Thing A is on fire so it's fine for thing B to be on fire, too-style argumentation.

I know genomes. Don't delete your DNA

Too many people are panicking about 23andMe.

stevensalzberg.substack.com

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Austin Richardson @agdr.org · Jun 30

Q: what do viruses and potatoes have in common?
A: both are "acellular root"

Reposted by Austin Richardson

Andrew Rambaut @arambaut.bsky.social · Jun 23

Handy to keep up with the ICTV's changes to virus taxonomy and species names:
taxonomy.onecodex.com/taxon/694009...
vs:
taxonomy.onecodex.com/taxon/694009...
or
taxonomy.onecodex.com/taxon/11676/...
vs
taxonomy.onecodex.com/taxon/11676/...

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Reposted by Austin Richardson

Jonathan Jacobs @bioinformer.bsky.social · Jun 19

Are you attending #ASMicrobe this is week? Stop by my talk on Friday morning (10AM) and say hello! 👋 if you can’t make it and want to meet up - just drop me a DM!

I love this meeting and connecting with so many friends and colleagues over the years has made it really a special meeting.

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Austin Richardson @agdr.org · Jun 16

🌳 Taxonomy Time Machine now supports batch lookups! Quickly resolve lists of names/TaxIDs to their current NCBI taxonomy → taxonomy.onecodex.com/bulk-resolver

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Austin Richardson @agdr.org · May 24

🚀 Pushed some updates to taxonomy.onecodex.com

- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements

Taxonomy Time Machine

Explore and compare the history of the NCBI Taxonomy Database. Instantly browse, search, and reconstruct taxonomic lineages at any point in time. Open source, web-based, and API-accessible.

taxonomy.onecodex.com

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Reposted by Austin Richardson

Jonathan Jacobs @bioinformer.bsky.social · Apr 2

🧵 The ATCC Genome Portal hit 5,500 authenticated microbial genomes (>2,600 species)! 🎉🥳 We've sequenced, assembled, annotated 4,538 bacteria, 479 viruses, 479 fungi, and 4 protists! All NGS in-house @ ATCC under ISO, and >90% on BOTH @nanoporetech.com and #Illumina 😎 www.atcc.org/applications...

Discover the ATCC Genome Portal | ATCCCart

www.atcc.org

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Austin Richardson @agdr.org · Apr 2

Something happened to my $PATH and now nothing works

Trisolarans: “the Sophons have succeeded in disrupting science”

Austin Richardson @agdr.org · Mar 24

Bad day for VCF files

Reposted by Austin Richardson

Kai Blin @kblin.bsky.social · Mar 2

It's clearly a DNS issue, but overall, the NCBI is the least reliable I've ever experienced in my career. And I'm in this long enough to remember the Entrez API giving you only part of the file every 50-100th time.

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Austin Richardson @agdr.org · Feb 15

using github copilot to fail at github workflows aka boiling the ocean

Austin Richardson @agdr.org · Feb 11

I call it the London Smaug (Tension Tamer + espresso latte)

Reposted by Austin Richardson

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Feb 11

Join us at SNU and gain access to leading-edge hardware: m.youtube.com/watch?v=ztth...

Mac OS9 for Bioinformatics in SNU

YouTube video by 갈로아 Galois

m.youtube.com

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Austin Richardson @agdr.org · Feb 5

How many arginines are in mStrawberry?