Bioinformatics rewrites miss the relational impact tofolks that are still actively maintaining and developing the software. I've been guilty of this myself, and I'll be sharing my story soon so others can learn from it.
Benjamin J. Buchfink
@bbuchfink.bsky.social
Independent scientist, Tübingen, Germany. Developer of the DIAMOND protein aligner. https://github.com/bbuchfink/diamond https://www.linkedin.com/in/benjamin-j-buchfink-875692105
![Comic. [Person 1 with short hair on stage behind podium reading off paper while addressing audience. People are shown sitting in chairs while Person 2 with ponytail and Person 3 waving are walking toward stage.] PERSON 1: This year’s Nobel Prize in “calibrating your equipment carefully and not embarrassing yourself by publishing spurious results” goes to Dr. Adams and Dr. Smith, who did *not* announce the discovery of microbes on Titan. PERSON 3: Thank you, thank you.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreihztdrvxjeyzmz6dmz3xb4vi6wiwwtge6fwdoxjcum5aptndv3kfm)
A few additional thoughts following my post: 1. There's likely far more biological data than we often assume. The challenge's that it remains highly fragmented. Large international efforts to integrate them could greatly advance understanding of complex, dynamic biological systems.
César de la Fuente@delafuentelab.bsky.social · 2w agoBiology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...
Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...
AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics
Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...
biorxiv.org
Ten quick tips to SNIFF out sustainable and secure scientific software journals.plos.org/ploscompbiol... 🧬💻🧪
Ten quick tips to SNIFF out sustainable and secure scientific software
Modern computational biology depends heavily on open-source software tools, analysis pipelines, and containerized workflows developed and shared by the research community. While there is extensive gui...
journals.plos.org
This was a fun one to write. Partly because of the subject, mostly because of the @uvadatascience.bsky.social people I wrote it with 🧑💻 blog.stephenturner.us/p/how-to-sni...
How to SNIFF out Good Scientific Software
New PLOS Computational Biology paper: "Ten Quick Tips to SNIFF Out Sustainable and Secure Scientific Software"
blog.stephenturner.us
DIAMOND v2.2.4 is available today, providing compositional matrix adjust for the clustering workflows and more. github.com/bbuchfink/di...
GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.
Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond
github.com
New study by Alexander Henoch (@ahenoch.bsky.social), a PhD student in our group @hifmb.de and @awi.de, shows what it takes to bring gene synteny into microbial pangenomes, and what we learn about the variability landscape of genomes when we do that. See the pre-print here: doi.org/10.64898/202...
Few people know that BLASTP applies SEG masking to the target sequences by default github.com/bbuchfink/di...
BLAST SEG masking
Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond
github.com
OrthoFinder v3: a tool for phylogenetic orthology inference with boosted accuracy and scalability for massive datasets. @lauriebelch.bsky.social @stevenkelly.bsky.social @jonathancholmes.bsky.social @yiliu88.bsky.social www.nature.com/articles/s41...
OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature Methods
The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.
nature.com
The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...
OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature Methods
The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.
nature.com
Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social
sandpiper
sandpiper.qut.edu.au
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
npr.org
Honored to announce that DIAMOND is one of 52 benchmarks in SPEC CPU®2026 🥳🎉🥂https://arxiv.org/abs/2605.01575
SPEC CPU: The Next Generation
The march toward developing relevant and robust CPU benchmarks continues with the introduction of SPEC CPU 2026, the next generation suite for measuring processor performance. This paper details the m...
arxiv.org
This is now published in Genome Research (doi.org/10.1101/gr.2...). Thank you everyone for your feedback and also the anonymous reviewers who helped to greatly improve the paper. I hope this becomes a useful resource for the community.
Hash functions in nucleotide sequence analysis
Randomness is a powerful tool in the design and analysis of algorithms and data structures for nucleotide sequence data. Nucleotide sequences are not themselves random but are often randomized using hash functions. Despite their widespread use in genomics, there is no comprehensive review of the types of hash functions used and their various applications. In this survey intended for bioinformatic methods developers, we divide hash functions into four categories: scattering hash functions, permutations, minimum perfect hash functions, and locality-sensitive hash functions. For each category, we provide examples of both general-use hash functions that have been applied in nucleotide sequence analysis and hash functions that have been designed specifically for nucleotide sequence analysis. We highlight their salient properties, commonalities, differences, and application areas.
doi.org
PPaul Medvedev @pashadag.bsky.social · last yr.
1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.
Tiberius 2.0.0 is out 🎉 Now supports 7 eukaryotic clades, covering ~92% of NCBI assemblies. Modular rewrite + ~30% faster runtime. Benchmarks included, more soon. Thanks to Lars Gabriel, Richard Krieg & Felix Becker 🙌 github.com/Gaius-August... #bioinformatics #genomics #genomeannotation
GALBA2 walks into the arena. We rewrote our protein-based genome annotation pipeline in Snakemake. Give it a genome + proteins from close relatives → get gene predictions. No RNA-Seq, no GeneMark needed. miniprot → AUGUSTUS, fully containerised, HPC-ready. github.com/Gaius-Augustus/GALBA2
1/ BRAKER4 hatched! The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...
I'm not looking forward to a future where all the tools are being vibe-rewritten into languages people don't want to learn. Who will maintain all this? The original maintainers won't. It's not the language they were comfortable with. Does the prompter understand the tool well enough?
Phil Ewels@ewels.bsky.social · 4mo agoSuper excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀 I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵 seqeralabs.github.io/RustQC/
DIAMOND DeepClust: an ultrafast clustering method for organizing the protein universe of life. www.nature.com/articles/s41...
Clustering the protein universe of life using DIAMOND DeepClust - Nature Methods
DIAMOND DeepClust provides an ultra-fast clustering method for organizing the protein universe of life at low sequence identity, enabling large-scale dimensionality reduction and improving downstream ...
nature.com
Clustering proteins using DIAMOND is out now @natmethods.nature.com www.nature.com/articles/s41...
Clustering the protein universe of life using DIAMOND DeepClust - Nature Methods
DIAMOND DeepClust provides an ultra-fast clustering method for organizing the protein universe of life at low sequence identity, enabling large-scale dimensionality reduction and improving downstream ...
nature.com
We just released #anvio v9, "eunice" 🎉 This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176. Read the release notes: github.com/merenlab/anv... Visit our up-to-date web page: anvio.org
The 2026 Workshop on Genomics comes to an end! It has been two intense and inspiring weeks of Genomics in Český Krumlov. We hope everyone is going back home with a renewed excitement for science and new friends and collaborations around the world! 🙆🏻♀️🧬 #evomics2026
DIAMOND v2.1.17 has new output fields sRANK to print taxonomy nodes of the given rank associated with the subject sequence, where RANK can be any rank in the NCBI taxonomy, e.g. sdomain, skingdom, sphylum, sorder, sgenus, sspecies, etc. github.com/bbuchfink/di...
GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.
Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond
github.com
I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI
Recurse Center@recurse.com · 9mo agoWhat’s the lore behind choosing your career path ?
DIAMOND v2.1.15 now supports all taxonomy features for BLAST databases, and support for using BLAST databases has also been added to the Bioconda version github.com/bbuchfink/di...
GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.
Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond
github.com
