🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12
Over the last 30 years, RECOMB Proceedings were published by Springer and ACM. On the other hand, full versions of selected papers appeared in various journals. This caused confusion in locating RECOMB publications.
Preprint Alert! With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression! A thread:
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 10mo agoInverted colored de Bruijn Graph for practical kmer sets storage https://www.biorxiv.org/content/10.64898/2025.12.08.692073v1
Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6) 👉 Preprint www.biorxiv.org/content/10.1... 👉 Github github.com/rolandfaure/...
Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching
We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...
biorxiv.org
🌎👩🔬 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...
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
Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...
🧬 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
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
🚨 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/
Do you want to learn systematic ways in which you can revise your research papers? I've posted a short collection of 4 lectures youtube.com/playlist?lis... 1/n
Writing in Computer Science - YouTube
This is a small collection of videos for learning about how to write research papers in computer science. For now, it contains four basic lectures, with more...
youtube.com
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-...
