Giulio Ermanno Pibiri

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.

Ahah crazy!

Cool! Didn’t know :)

what conf are you attending?

Very strange that ArXiv did not accept this review paper. I also recently (some months ago) uploaded a survey on ArXiv and the process went smooth. I suspect there must be other reasons for their decision…

If I remember correctly, this idea was already used in Cortex or McCortex indices by Z. Iqbal et al.

Very interesting opportunity!

Ah yeah interesting! I remember I also wanted to try something...and reordering by minimizer content came immediately to mind.

Yes, I agree. Without consulting online forums -- and now, asking ChatGPT -- it's impossible to remember even how to do a basic thing. CMake generates make files. Can we develop a tool that generates the CMake files that generate the make files?! :D

😂 yeeee

Interesting! Cc @ale-campa.bsky.social

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

Hashed sorting is typically faster than hash tables Benchmarks and theoretical explanation of why and when hashed radix sort beats hash tables.

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

Wow, fantastic guys! Congratulations and finger crossed! :)

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.

As in previous years, the workshop will be free to attend, but *registration will be required* in order to participate. The call for abstracts will be announced around mid-November, and registrations will open shortly thereafter. Can't wait to meet you all in Venice :)

DSB is an annual scientific meeting at the crossroads of computer science and biology. It is the unique forum to discuss compact data structures and their applications for processing data from life sciences.

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!

GitHub - RagnarGrootKoerkamp/sassy: Fast approximate string searching Fast approximate string searching. Contribute to RagnarGrootKoerkamp/sassy development by creating an account on GitHub.

Just released Sassy 0.1.4, which now supports macos/arm NEON instructions :)

Also some smaller fixes by @tfenne.bsky.social.

github.com/RagnarGrootK...

Release Version 4.0.0 · jermp/sshash What's Changed General renaming of functions/methods and project structure (e.g., now main tools are in a folder named tools). Added CI workflows. Refactored CMakeLists.txt: added option to suppor...

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 ☺️

AllTheBacteria - all bacterial genomes assembled, available and searchable The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...

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...

Congratulations Ragnar!! 🎉

I only see an improvement for k=63; storing minimizer positions don’t give a similar improvement for k=31. I don’t see any immediate explanation, especially given that the extension rate and other query statistics are identical… for a potential paper, we should find an explanation 😌

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

These are the commits that we love ❤️ the most productive ones are those that remove code :)

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!