Austin Richardson @agdr.org · 14/08/2026we did we all switch to the >$20/mo IDE with only one syntax highlighting theme? 010
Austin Richardson @agdr.org · 19/06/2026this entire repo could be a markdown file github.com/DietrichGebe...github.comGitHub - DietrichGebert/ponytail: Makes your AI agent think like the laziest senior dev in the room. The best code is the code you never wrote.Makes your AI agent think like the laziest senior dev in the room. The best code is the code you never wrote. - DietrichGebert/ponytail 020
Reposted by Austin RichardsonSamuel Lampa @smllmp.bsky.social · 15/05/2026A bit intrigued how useful the combination of a bit of coloring, formatting + a really fast terminal app (alacritty), can be for visually inspecting reads. This one had me realize these are all pretty much the same (contaminating) sequence 👇 051
Austin Richardson @agdr.org · 14/05/2026Taxonomy Time Machine now shows merges taxonomy.onecodex.com 083
Reposted by Austin RichardsonTorsten Seemann @torstenseemann.bsky.social · 15/12/2025💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...github.comRelease Heading into the sunset · tseemann/prokkaThe future This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen... 311959
Reposted by Austin RichardsonAntonio 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... 49047
Reposted by Austin RichardsonMichael Baym @baym.lol · 26/10/2025When you buy a cutting board from bioinformaticians 5557
Reposted by Austin Richardson🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 25/09/2025Apple'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...genomely.substack.comSimpleFold and the Future of Protein FoldingA Generative Shift in Protein Folding 1153
Reposted by Austin RichardsonPaul Medvedev @pashadag.bsky.social · 25/09/2025If 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. 9133
Austin Richardson @agdr.org · 15/09/2025they should invent a type of volatile memory that gets heavier the more data it contains 000
Reposted by Austin RichardsonBede Constantinides @bede.im · 12/09/2025Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...log.bede.imZstandard's long range mode works wonders for genome sequences* 0189
Austin Richardson @agdr.org · 31/08/2025NCBI BLAST can now output a proper CSV with headers 👏🎉: www.ncbi.nlm.nih.gov/books/NBK131...ncbi.nlm.nih.govBLAST+ Release NotesNote: If building BLAST+ from source code, the Zlib, Zstandard and Bzip2 libraries will be needed. 020
Austin Richardson @agdr.org · 25/08/2025you can just pour milk over trail mix and eat it like cereal 000
Austin Richardson @agdr.org · 18/08/2025"You are standing in an open field west of a white house, with a boarded front door." 110
Reposted by Austin RichardsonRagnar {Groot Koerkamp} @curiouscoding.nl · 06/08/2025Little 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-... 1175
Reposted by Austin RichardsonDr. Stephanie @punkrockscience.bsky.social · 23/07/2025I do not enjoy that we now live in a world where seeing this banner at the top of PubMed makes me nervous. 25011
Reposted by Austin RichardsonAlex Crits-Christoph @acritschristoph.bsky.social · 22/07/2025TIL 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: 1218
Reposted by Austin RichardsonPhilipp Bayer @philippbayer.bsky.social · 22/07/2025This 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.stevensalzberg.substack.comI know genomes. Don't delete your DNAToo many people are panicking about 23andMe. 111
Austin Richardson @agdr.org · 30/06/2025Q: what do viruses and potatoes have in common? A: both are "acellular root" 000
Reposted by Austin RichardsonAndrew Rambaut (🐏🎀) @arambaut.bsky.social · 23/06/2025Handy 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/...taxonomy.onecodex.comTaxonomy Time MachineExplore 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. 052
Reposted by Austin RichardsonJonathan Jacobs @bioinformer.bsky.social · 19/06/2025Are 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. 1135
Austin Richardson @agdr.org · 16/06/2025🌳 Taxonomy Time Machine now supports batch lookups! Quickly resolve lists of names/TaxIDs to their current NCBI taxonomy → taxonomy.onecodex.com/bulk-resolver 041
Austin Richardson @agdr.org · 24/05/2025🚀 Pushed some updates to taxonomy.onecodex.com - Example queries to help you get started - Summary section for easier interpretation - Perf. improvementstaxonomy.onecodex.comTaxonomy Time MachineExplore 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. 065
Reposted by Austin RichardsonJonathan Jacobs @bioinformer.bsky.social · 02/04/2025🧵 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...atcc.orgDiscover the ATCC Genome Portal | ATCCCart 23212
Austin Richardson @agdr.org · 02/04/2025Something happened to my $PATH and now nothing works Trisolarans: “the Sophons have succeeded in disrupting science” 000
Reposted by Austin RichardsonKai Blin @kblin.bsky.social · 02/03/2025It'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. 011
Austin Richardson @agdr.org · 15/02/2025using github copilot to fail at github workflows aka boiling the ocean 020
Austin Richardson @agdr.org · 11/02/2025I call it the London Smaug (Tension Tamer + espresso latte) 020
Reposted by Austin RichardsonMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 11/02/2025Join us at SNU and gain access to leading-edge hardware: m.youtube.com/watch?v=ztth...m.youtube.comMac OS9 for Bioinformatics in SNUYouTube video by 갈로아 Galois 4333
Austin Richardson @agdr.org · 03/02/2025I’m not familiar with that DB myself so I’m not sure if those are the right files. The NCBI Pathogens page links to that directory though. 110
Austin Richardson @agdr.org · 03/02/2025do you know if everything is in here? ftp.ncbi.nlm.nih.gov/pathogen/ftp.ncbi.nlm.nih.govIndex of /pathogen 110
Austin Richardson @agdr.org · 26/01/2025Can you share the ISOs? Maybe on archive.org?archive.orgInternet Archive: Digital Library of Free & Borrowable Texts, Movies, Music & Wayback Machine 100
Reposted by Austin RichardsonFlo Débarre @flodebarre.eurosky.social · 11/01/2025Five years ago (Saturday 11 Jan 2020), first public announcement and availability of a sequence of the new coronavirus. It was posted by @eddieholmes.bsky.social at 01:05 UTC on Virological, and announced on Twitter at 01:08 UTC. ▫️1/ web.archive.org/web/20200118... archive.is/z880d 417071
Reposted by Austin RichardsonAndrew Page @andrewjpage.bsky.social · 10/01/2025I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e 2810760
Reposted by Austin RichardsonTitus Brown @titus.idyll.org · 27/12/2024Hi all, here's my passion project for December - a Web site for ~realtime DNA sample screening/composition analysis. Let me know what you think!ivory.idyll.orgAnnouncing: the chill-filter Web site - DNA sample composition at a glance!what's in my sample, dude? 37717
Reposted by Austin RichardsonNiema Moshiri @niema.net · 23/12/2024Got something interesting cooking up... 👀 @robert.bio 6404
Reposted by Austin RichardsonWei Shen 沈 伟 @shenwei356.bsky.social · 18/12/2024The story behind Sylph, from @jimshaw.bsky.social . It's quite inspiring to read. jim-shaw-bluenote.github.io/blog/2024/de...jim-shaw-bluenote.github.io Developing sylph - a look into bioinformatics tool development | Jim Shaw Jim Shaw's academic website. 2329
Reposted by Austin RichardsonMolly White @molly.wiki · 17/12/2024As the writer of an email newsletter, I perhaps ironically also much prefer RSS. For what it’s worth, an increasing number of RSS readers have functionality to receive email newsletters and plonk them into your feeds, and there are services like kill-the-newsletter.comkill-the-newsletter.comKill the Newsletter!Convert email newsletters into Atom feeds 2373
Reposted by Austin RichardsonZamin Iqbal @zaminiqbal.bsky.social · 13/12/2024Ha, a taxonomy time machine. I bet it has fun with with virus names over coming months 1226
Austin Richardson @agdr.org · 13/12/2024NCBI'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... 0217
Austin Richardson @agdr.org · 20/11/2024They're both "superseded by newer assembly for species" - www.ncbi.nlm.nih.gov/datasets/gen... - www.ncbi.nlm.nih.gov/datasets/gen... I think this suppression reason is specific to Euks because I don't see it for Bacteria. I guess, unlike bacteria, RefSeq doesn't include multiple refs per species 120
![screenshot of Eddie Holmes' tweet:
@edwardcholmes
All, an initial genome sequence of the coronavirus associated with the Wuhan outbreak is now available at Virological.org here: [link to virological]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:yqxcc5ayxllwkvel4narbha4/bafkreif5tqxzjq4jcbdixilkvf74b626h34s2voszstutwib2wgtk5wkqa)
