The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

❗ I clearly consider this result as THE most important result achieved over this last decade for exploiting and democratizing genomic data.
I think there will be a "before" and an "after" logan and logan-search
github.com/IndexThePlan...
logan-search.org
Have a look at this thread

📜 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

Maybe the simplest idea to decrease overestimations of a counting bloom filter. A trivial observation + 10 lines of code.
I'm surprised it has not been described before. Please comment if this is not the case.
Blog post here:
pierrepeterlongo.github.io/2025/03/17/m... 🧪🧬🖥️

Today I wanted to know the number of unique 27-mers in the hg38 human genome (spoiler there are 2.49 billion). I found no tool for doing this. So I wrote that github.com/pierrepeterl...

It may help.
Please use it / improve it.

🧬💻 #bioinformatics

We are back in the Town Theatre for a great lecture on Alignment, by @rayanchikhi.bsky.social! 🧬💻 #evomics2025 #genomics #bioinformatics

bsky.app/profile/pier...
Applications for this position are still open. If you're passionate about large-scale science, we'd love to hear from you.
🧬 & 🖥️

🚨🚨🚨
We are hiring
🚨🚨🚨

After the creation of logan-search (see: bsky.app/profile/pier...) we propose a 2-years engineer position for continuing the development and optimizations.

With @rayanchikhi.bsky.social and @tlemane.bsky.social

Details + applications: recrutement.inria.fr/public/class...

🚨 Call for Papers: RECOMB-seq 2025 🚨

🗓️ Dates: April 24-25, 2025

📍 Location: Seoul, South Korea

Key deadlines:
🔹 Abstract registration: Jan 24, 2025
🔹 Submission: Jan 31, 2025

More details: recomb-seq.github.io/papers/

🗓️Tomorrow, Friday December 13, Khodor HANNOUSH, from the @genscaleteam.bsky.social team, will defend his thesis entitled “Dynamic Pan-genome Graphs”. Details by following this link:

www.irisa.fr/date/2024-12...

Amazing ideas here www.biorxiv.org/content/bior... from
@yoann.bsky.social
and collaborators.

Reorganize minimizers to allow kmers dichotomic search. That's brilliant.

#bioinformatics 🧬🖥️

I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics)

go.bsky.app/TRWCnZs

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience