Lightnews — Scholar-powered news

Giulio Ermanno Pibiri @jermp.bsky.social · 5d

Ahah crazy!

1 1

Giulio Ermanno Pibiri @jermp.bsky.social · 6d

Cool! Didn’t know :)

1

Giulio Ermanno Pibiri @jermp.bsky.social · 6d

what conf are you attending?

1

Giulio Ermanno Pibiri @jermp.bsky.social · 10d

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…

1 2

Giulio Ermanno Pibiri @jermp.bsky.social · 21d

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

1

Giulio Ermanno Pibiri @jermp.bsky.social · 21d

Very interesting opportunity!

John Lees @bacpop.org · 21d

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

EMBL International PhD Programme – Unique in the world and waiting for you!

www.embl.org

Giulio Ermanno Pibiri @jermp.bsky.social · 26d

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

1

Giulio Ermanno Pibiri @jermp.bsky.social · 28d

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

4

Giulio Ermanno Pibiri @jermp.bsky.social · 28d

😂 yeeee

1

Giulio Ermanno Pibiri @jermp.bsky.social · 29d

Interesting! Cc @ale-campa.bsky.social

1

Giulio Ermanno Pibiri @jermp.bsky.social · 29d

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

Camille Marchet ⚡ @camillemrcht.bsky.social · 29d

Yohan Hernandez-Courbevoie chaired by Maxime Crochemore just before presenting REINDEER2 at #SPIRE2025 in London

4

Reposted by Giulio Ermanno Pibiri

Rob Patro @robp.bsky.social · Sep 8

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

3 15

Giulio Ermanno Pibiri @jermp.bsky.social · Sep 6

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

1 2

Reposted by Giulio Ermanno Pibiri

Ragnar {Groot Koerkamp} @curiouscoding.nl · Sep 4

Paraseq 0.4 is out now! With double the throughput for processing paired-end input :)

github.com/noamteyssier...

8 15

Giulio Ermanno Pibiri @jermp.bsky.social · Sep 4

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

1 4

Giulio Ermanno Pibiri @jermp.bsky.social · Sep 1

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 :)

1

Giulio Ermanno Pibiri @jermp.bsky.social · Sep 1

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.

1 1

Giulio Ermanno Pibiri @jermp.bsky.social · Sep 1

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

1 8 14

Reposted by Giulio Ermanno Pibiri

Rob Patro @robp.bsky.social · Aug 30

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!

5 19

Reposted by Giulio Ermanno Pibiri

Ragnar {Groot Koerkamp} @curiouscoding.nl · Aug 30

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

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

1 4 11

Giulio Ermanno Pibiri @jermp.bsky.social · Aug 28

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

2 6

Giulio Ermanno Pibiri @jermp.bsky.social · Aug 28

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...

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

30 67

Giulio Ermanno Pibiri @jermp.bsky.social · Aug 27

Congratulations Ragnar!! 🎉

1 1

Giulio Ermanno Pibiri @jermp.bsky.social · Aug 23

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 😌

1

Giulio Ermanno Pibiri @jermp.bsky.social · Aug 23

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

1 3 13