Giulio Ermanno Pibiri
@jermp.bsky.social
Associate Prof. of CS at Ca' Foscari University of Venice. Indexing, Data Compression, Algorithms.
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.
5/6 On the 466 haplotypes from the 2nd release of HPRC, the fastest Movi 2 index is under 50 GB. It can be reduced to 24 GB while remaining over 3x faster than SPUMONI. Movi 2 is smaller and faster than ropebwt3, although it computes PMLs, which are easier to get than the SMEMs found by ropebwt3.
October 22, 2025 at 7:41 AM
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.
Reposted by 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! 🖥️🧬
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 10, 2025 at 1:02 PM
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.
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
Postdoc Description.docx
Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...
docs.google.com
October 9, 2025 at 6:45 AM
Wow! You should definitely consider applying. Rob is an amazing scientist and professor, and a leader in the field.
Very interesting opportunity!
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
EMBL International PhD Programme – Unique in the world and waiting for you!
www.embl.org
September 17, 2025 at 6:23 PM
Very interesting opportunity!
Oh right, this is the SPIRE week! Enjoy SPIRE everyone and congrats to all contributors :)
Yohan Hernandez-Courbevoie chaired by Maxime Crochemore just before presenting REINDEER2 at #SPIRE2025 in London
September 9, 2025 at 11:40 AM
Oh right, this is the SPIRE week! Enjoy SPIRE everyone and congrats to all contributors :)
Reposted by Giulio Ermanno Pibiri
Hashing vs. sorting; interesting! reiner.org/hashed-sorting. Also I wonder if, depending on your use case, semi-sorting provides an even greater benefit? 🧬🖥️
Hashed sorting is typically faster than hash tables
Benchmarks and theoretical explanation of why and when hashed radix sort beats hash tables.
reiner.org
September 8, 2025 at 12:37 PM
Hashing vs. sorting; interesting! reiner.org/hashed-sorting. Also I wonder if, depending on your use case, semi-sorting provides an even greater benefit? 🧬🖥️
Reposted by Giulio Ermanno Pibiri
Paraseq 0.4 is out now! With double the throughput for processing paired-end input :)
github.com/noamteyssier...
github.com/noamteyssier...
September 4, 2025 at 10:41 PM
Paraseq 0.4 is out now! With double the throughput for processing paired-end input :)
github.com/noamteyssier...
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.
Package Recipe 'sshash' — Bioconda documentation
bioconda.github.io
September 4, 2025 at 7:12 AM
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
DSB 2026 Venice - February 18-19
Workshop Data Structures in Bioinformatics
dsb-meeting.github.io
September 1, 2025 at 6:10 PM
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
Reposted by Giulio Ermanno Pibiri
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!
August 30, 2025 at 1:53 PM
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!
Reposted by Giulio Ermanno Pibiri
Just released Sassy 0.1.4, which now supports macos/arm NEON instructions :)
Also some smaller fixes by @tfenne.bsky.social.
github.com/RagnarGrootK...
Also some smaller fixes by @tfenne.bsky.social.
github.com/RagnarGrootK...
GitHub - RagnarGrootKoerkamp/sassy: Fast approximate string searching
Fast approximate string searching. Contribute to RagnarGrootKoerkamp/sassy development by creating an account on GitHub.
github.com
August 30, 2025 at 1:26 PM
Just released Sassy 0.1.4, which now supports macos/arm NEON instructions :)
Also some smaller fixes by @tfenne.bsky.social.
github.com/RagnarGrootK...
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 ☺️
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...
github.com
August 28, 2025 at 5:09 PM
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
August 28, 2025 at 12:16 PM
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...
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
August 23, 2025 at 10:51 AM
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
My collaborator (whom I just met in person today) and @jermp.bsky.social's student, @ale-campa.bsky.social presenting "Fast pseudoalignment queries on compressed colored de Bruijn graphs"! #WABI25
August 21, 2025 at 6:58 AM
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
Reposted by Giulio Ermanno Pibiri
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 2025
WABI Conference on Algorithms in Bioinformatics
wabiconf.github.io
August 20, 2025 at 2:45 AM
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!
🧬🖥️ We are thrilled to be hosting the 25th International Conference on Algorithms for Bioinformatics (WABI 2025) next week at UMD! Look at this amazing lineup of proceedings papers: drops.dagstuhl.de/entities/vol...
25th International Conference on Algorithms for Bioinformatics (WABI 2025)
drops.dagstuhl.de
August 16, 2025 at 12:14 PM
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! 🎉
Congratulations to Rayan Chiki, (Institut Pasteur) head of the “Sequence Bioinformatics” unit, for securing the ERC Proof of Concept 2025 for his project ENZYMINER! 👏
@rayan.chiki.bsky.social
#Bioinformatics
@rayan.chiki.bsky.social
#Bioinformatics
July 25, 2025 at 3:32 PM
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.
July 24, 2025 at 9:19 AM
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 :)
Congrats to @curiouscoding.nl for getting the #SEA2025 best paper award for his work on PtrHash!
drops.dagstuhl.de/entities/doc...
drops.dagstuhl.de/entities/doc...
PtrHash: Minimal Perfect Hashing at RAM Throughput
Feedback for Dagstuhl Publishing
drops.dagstuhl.de
July 24, 2025 at 8:34 AM
Well deserved indeed! Looking forward to chairing the session :)
Congratulations Ben! Fantastic news!
Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬
July 22, 2025 at 7:29 PM
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...
jermp.github.io/assets/pdf/s...
jermp.github.io
July 22, 2025 at 4:10 PM
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...
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!
After a long wait, the newest version of piscem-infer is out (github.com/COMBINE-lab/...). This version adds range factoized equivalence classes (academic.oup.com/bioinformati...). Piscem-infer should be used following piscem for mapping (with the map-bulk command). 1/2
Release v0.7.0 · COMBINE-lab/piscem-infer
Install piscem-infer 0.7.0
Install prebuilt binaries via shell script
curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem-infer/releases/download/v0.7.0/piscem-infer-install...
github.com
July 20, 2025 at 3:58 PM
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!
Reposted by Giulio Ermanno Pibiri
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...
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...
July 18, 2025 at 8:20 PM
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...
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 deadline for poster abstracts (and early registration) for WABI 2025 is coming up soon (July 20th AoE)! Make sure to submit your posters and register at the early registration rate!
Abstract submission site: easychair.org/conferences/...
Conference website: wabiconf.github.io/2025/
Abstract submission site: easychair.org/conferences/...
Conference website: wabiconf.github.io/2025/
Log in to EasyChair for WABI 2025
easychair.org
July 16, 2025 at 7:02 PM
Last-minute opportunity to disseminate your new algorithm in Comput. Bio! Submit guys :)