Rayan Chikhi
@rayanchikhi.bsky.social
510 followers 95 following 18 posts
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rayanchikhi.bsky.social
There's a typo on line 225, it is actually 50% identity, not 90%. But yeah, SRA is highly redundant :)
rayanchikhi.bsky.social
Earth’s genetic diversity is a heritage of humanity. It has been an honour to explore this data with a team of dedicated scientists who shared our vision of making this data free and accessible to all 🌍🧬❤️ Thank you!

Updated preprint: doi.org/10.1101/2024...
rayanchikhi.bsky.social
This is a new frontier for biological discovery and AI training data. Logan expands the universe of known proteins, plasmids, AMR, P4 satellites, and the newly discovered Obelisk RNA elements.
rayanchikhi.bsky.social
All Logan data is freely-available (cc0) right now. We show how Logan-Search (www.logan-search.org) can be used to uncover viral reactivation (HHV-6) in cell therapy products (TIL and CAR-T).
rayanchikhi.bsky.social
Logan rapidly accesses the tapestry of Life’s genetic diversity and can help solve global issues.

To tackle the microplastic crisis, we searched Logan for new versions of the 213 known plastic-degrading enzymes. We identified 200+ million homologs 🤯, including new high-efficiency enzymes 🥤🔥
rayanchikhi.bsky.social
Logan enables minute-scale k-mer search, and hour-scale deep homology protein alignment search, across 100+ Billion proteins.

www.logan-search.org
rayanchikhi.bsky.social
One year after our initial preprint, we're excited to post a major update to Logan.

At its heart, Logan is the assembly of 27 million samples (50 Pbp) using a 6-day cloud-compute peaking at 2.2M vCPUs. This compresses the SRA 140x compared to raw FASTQs.

github.com/IndexThePlan...
rayanchikhi.bsky.social
🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...
Reposted by Rayan Chikhi
pasteur.fr
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
rayanchikhi.bsky.social
Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...
Reposted by Rayan Chikhi
camiladuitama.bsky.social
🧬 Excited to share our latest work, MUSET 🌭, a new tool for creating abundance unitig matrices from sequencing data. It was published yesterday in Oxford Bioinformatics if you want to have a look👀 :

academic.oup.com/bioinformati...

Let's break it down:
MUSET: Set of utilities for constructing abundance unitig matrices from sequencing data
AbstractSummary. MUSET is a novel set of utilities designed to efficiently construct abundance unitig matrices from sequencing data. Unitig matrices extend
academic.oup.com
rayanchikhi.bsky.social
For more context: Logan is a collection of all public sequencing data (until end of 2023) assembled into contigs. It is freely hosted on the cloud, and contains hundreds of terabytes of valuable genomic data: github.com/IndexThePlan...
GitHub - IndexThePlanet/Logan: Logan Unitigs and Contigs
Logan Unitigs and Contigs. Contribute to IndexThePlanet/Logan development by creating an account on GitHub.
github.com
rayanchikhi.bsky.social
We have updated all Logan contigs (now at version 1.1)! Contiguity has been much improved (2x) and a duplicated k-mers bug has been fixed. More information and changelog here: github.com/IndexThePlan...
github.com
Reposted by Rayan Chikhi
recombseq.bsky.social
🚨 Keynotes at RECOMB-seq 2025! 🚨

🌟 Alicia Oshlack – computational transcriptomics
@aliciao.bsky.social

🌟 Rayan Chikhi – sequencing data structures
@rayanchikhi.bsky.social

🗓️ Dates: April 24–25, 2025
📍 Seoul, South Korea

recomb-seq.github.io/speakers/
Reposted by Rayan Chikhi
martinsteinegger.bsky.social
Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web.
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...