Now also on arxiv: arxiv.org/abs/2602.04103

Nice work @npmalfoy.bsky.social! Can't wait for this at DSB :)

Deadline for registration is Jan 31. Don’t miss it! See you all in beautiful Venice 😉

This preprint significantly improves the original design of SSHash to accelerate query and construction time. Looking back at one’s own work is very important and sometimes surprising ☺️

Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster! www.biorxiv.org/content/10.6...

The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/

Congratulations to @brinda.eu and Francesca for this impressive work!! We will surely give you a hand in integrating the latest Fulgor version, which is considerably faster thanks to @ale-campa.bsky.social.

Great work and congrats to all authors! 🥳 Can't wait to read the preprint. Just for reference: a Fulgor index ⚡ on the same HPRC collection takes 8.26 GB (not in its most succinct representation). Fulgor, however, can be regarded as a "lossy" method here since it is based on kmers.

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Wow! You should definitely consider applying. Rob is an amazing scientist and professor, and a leader in the field.

Very interesting opportunity!

Oh right, this is the SPIRE week! Enjoy SPIRE everyone and congrats to all contributors :)

Hashing vs. sorting; interesting! reiner.org/hashed-sorting. Also I wonder if, depending on your use case, semi-sorting provides an even greater benefit? 🧬🖥️

Paraseq 0.4 is out now! With double the throughput for processing paired-end input :) github.com/noamteyssier...

After requests from the community, SSHash lands on Bioconda package index: bioconda.github.io/recipes/ssha.... Cool! Thanks @robp.bsky.social for all the help and support.

We are glad to announce that the next workshop “Data Structures in Bioinformatics” (DSB 2026) will take place in Venice, Italy, on *February 18-19*, 2026. dsb-meeting.github.io/DSB2026/ Book the dates! #DSB26

Without our own users, I have no idea when I would have learned about this extremely subtle limitation of the minimap2 serialized index github.com/COMBINE-lab/... (reference names > 255 bytes don't roundtrip). Users push your software in ways you might not even think to!

Just released Sassy 0.1.4, which now supports macos/arm NEON instructions :) Also some smaller fixes by @tfenne.bsky.social. github.com/RagnarGrootK...

There we go: github.com/jermp/sshash.... What a big release! Many thanks to all contributors and people from the community for their suggestions. Happy to keep maintaining (and improving on) these tools ☺️

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :) www.biorxiv.org/content/10.1...

I'm about to release SSHash v4.0.0. More details in a future post. Among other things, now indexes store the pos. of minimizers instead of super-kmers. Compared to the latest post (last jun), this somehow had a very positive effect of streaming queries for larger k (e.g., 63)! ☺️ CC @robp.bsky.social

Wow, fantastic room: haven't seen so many screen for a single presentation at a CS conference! ☺️ @ale-campa.bsky.social has been doing some amazing development on the Fulgor index. Soon enough, more exciting news. Stay tuned! ⚡ 🧬 #WABI25

The 25th iteration of the excellent Conference for Algorithms in Bioinformatics (WABI) starts tomorrow at UMD @umdscience.bsky.social at the Brendan Iribe Center. You can find details at the website wabiconf.github.io/2025/. We'll use the tag #WABI25 for the meeting!

WABI is definitely my favourite annual meeting; the community is amazing. I won’t attend this year but @ale-campa.bsky.social will illustrate our latest development around the Fulgor ⚡️index: faster query algorithms this time! Don’t miss his talk!

Wow, congrats Rayan! 🎉

It was a great honour for me to introduce prof. Sebastiano Vigna today at SEA’25. His contributions to large-scale indexing are broad and far-reaching. Inspirational for future generations of computer scientists and professors.

Well deserved indeed! Looking forward to chairing the session :)

Congratulations Ben! Fantastic news!

Today was the first day at SEA'25 in Venice. I've presented the "U-index" framework :) Here are the slides from my talk + a short recap of the main highlights. 1/6 jermp.github.io/assets/pdf/s...

Better features for Piscem🐟 Check this out! Continuous tool maintenance and improvements is what makes a tool rock in the long term. Congrats @robp.bsky.social!

Sassy is out now! Ever need to search for approximate matches of short DNA strings? Sassy is the tool to use! Available now wherever you get your code With @rickbitloo.bsky.social curiouscoding.nl/papers/sassy... github.com/ragnarGrootK...

Last-minute opportunity to disseminate your new algorithm in Comput. Bio! Submit guys :)

The GreedyMini paper is finally out as part of #ISMBECCB2025 proceedings: academic.oup.com/bioinformati.... Arseny will present it on the last day (July 24th) and last session (14:20) of the HiTSeq meeting.

🖥️🧬: The ISMB 2025 proceedings are out! I’m looking forward to seeing many presentations on this work next week :). academic.oup.com/bioinformati...

My colleague asked me to circulate this job posting for Professor / Associate Professor in Computational Biology / Genomics at the University of Tokyo (P.S. I'm not affiliated): www.k.u-tokyo.ac.jp/en/informati...

Last afternoon in Tokyo 🇯🇵 It's been so nice to be back here again after 2018...Next time won't take 7 years 😅 @kampersanda.bsky.social

I gave an invited talk today in beautiful Tokyo for a workshop organized by Yasuo Tabei, at RIKEN AIP 🇯🇵. My slides are here jermp.github.io/assets/pdf/s.... This surveys recent development in indexing colored de Bruijn graphs in little space while supporting fast pseudoalignment.

🧬🖥️ In addition to an update to oarfish, a new version (0.14.0) of piscem (zenodo.org/records/1509...) has just been released. This version pulls in some of the latest improvements to sshash by @jermp.bsky.social! 1/2

🖥️🧬 WABI '25 will not only have excellent keynotes, but an exciting program of papers. The titles and abstracts of all accepted WABI '25 papers are now available on the conference website (wabiconf.github.io/2025/talks/). I'm looking forward to seeing these talks!

Being working on revising some parts of the SSHash software to bring performance improvements. Here are the results: much better construction performance and faster streaming queries.

A monumental collaborative effort with many incredible people ☺️ Proud to be part of this!

Promotion day! 😊

What makes good CS research? Surely novel ideas, broad impact, and rigorous methodology but -- also -- good software practices: modularity/simplicity/usability. Here is a nice such story 👇

📜 Excited to share insights from our recent paper: "Kaminari: a resource-frugal index for approximate colored k-mer queries". The study aims to efficiently identify documents containing a query string, focusing on DNA strings. www.biorxiv.org/content/10.1... 🧬 🖥️ 1/8

The open-closed mod-minimizer paper with @daniel-c0deb0t.bsky.social and @jermp.bsky.social was just published :) Here's a previous twitter thread we did: x.com/curious_codi... doi.org/10.1186/s130...

New minimizer-based index: the u-index! Tl;dr: Use your favourite text index on minimizer-sketch-space to locate long patterns using only small space. With many coauthors: Lorraine, Gabriele, Grigorios, @robp.bsky.social, @jermp.bsky.social, and Solon! arxiv.org/abs/2502.14488

Building on Algorithmica's post on S-trees and the famous "Array layouts for comparison based searching" paper, I did a little project on making an optimized implementation of the S+ tree. The result is 40x speedup over plain binary search! 🧵 curiouscoding.nl/posts/static...

Do you want to learn systematic ways in which you can revise your research papers? I've posted a short collection of 4 lectures youtube.com/playlist?lis... 1/n

🚨You've got to read this one. 🚨

Optimist: there is a 1/2-full cup Pessimist: there is a 1/2-empty cup Computer Scientist: oh look, O(1) full cups (also O(1) empty cups).