gaetanbenoit.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

It's the K-mer Days in Toulouse, a meeting between computational bioinformaticians and clinical bioinformaticians, discussing how k-mer based methods can be used in research/diagnostic... Here Yohan presents REINDEER2.

submitted 1 day ago • 1 comment

Really enjoying my first attendance at @mdc-bimsb.bsky.social in Berlin. Thanks for the invitation!

submitted 7 days ago • 1 comment

Preprint alert! 🦌 Our new abundance index, REINDEER2, is out! It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput. Short thread! www.biorxiv.org/content/10.1... github.com/Yohan-Hernan...

submitted 8 days ago • 1 comment

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

submitted 10 days ago • 0 comments

Verkko2 paper is finally published! genome.cshlp.org/content/earl...

submitted 14 days ago • 1 comment

Hey yeast lovers. Do you like pangenomes? O'Donnel et al. 2023 produced T2T assemblies of different strains, including phased haplotypes for yeast. Here I selected 10 phased haplotypes and the S288C reference, and looked for the MST28 / YAR033W gene reported to contain SVs such as indels. 👇🏻👇🏻

submitted 16 days ago • 2 comments

NEW PREPRINT OUT arxiv.org/abs/2506.04926 The Burrows-Wheeler transform of a string is, in general, more compressible than the original string, especially when it contains lots of repeated subtrings. The extended BWT allows to deal with multisets of strings. 1/7

submitted 21 days ago • 1 comment

Another circRNA in MAN1A2 human gene, first described in Mercer et al. 2015. I retrieved illumina data, built the graph, searched the gene in Vizitig and here it is!

submitted 24 days ago • 1 comment

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

submitted 24 days ago • 1 comment

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

submitted 30 days ago • 5 comments

📜 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

submitted 31 days ago • 1 comment

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

submitted 31 days ago • 4 comments

Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.

submitted 33 days ago • 1 comment

www.biorxiv.org/content/10.1... Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use) github.com/rrwick/Autoc...

submitted 42 days ago • 2 comments

In this (rebutted) grant proposal I wrote that I thought we could see circular RNAs with Vizitig, despite being hard to detect and with low expression. Guess what? Looks very much like a circular RNA to me 😎 (in TET2 gene, human co-assembled cancer RNA-seq samples).

submitted 52 days ago • 1 comment

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵

submitted 60 days ago • 5 comments

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

submitted 69 days ago • 5 comments

High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1

submitted 63 days ago • 0 comments

Starting #RECOMBseq with @rayanchikhi.bsky.social 's keynote. Here stressing our responsibility as scientists to enable access to a common good: genomic data

submitted 64 days ago • 1 comment

You should try A*PA2! It's Edlib, but faster! It's waiting for its first citation 😅

submitted 127 days ago • 1 comment

Finally; the preprint on Cuttlefish 3 is available! This is the most recent in a long line of work led by Jamshed Khan, a recent PhD graduate from my lab. Cuttlefish 3 further improves the efficiency of Cuttlefish 2, while adding support for colored compacted de Bruijn graphs. 1/x

submitted 141 days ago • 1 comment

🧬 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:

submitted 143 days ago • 1 comment

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...

submitted 144 days ago • 1 comment

After 24 years of work, I’m thrilled to announce the TYMEFLIES dataset, which comprises metagenomes from Lake Mendota (Madison, WI), collected roughly every 10 days (471 samples) for 20 years! @quendi.bsky.social @robinrohwer.bsky.social rdcu.be/d5put A thread…

submitted 175 days ago • 3 comments

How helpful is a de Bruijn graph for visualizing alternative RNA variants? Here I requested our graph visualization tool Vizitig to show me the CIC human gene in my data (3 RNA-seq samples). I connected sequences to known genes using an annotation and colored CIC's exons in different tints.

submitted 161 days ago • 1 comment

AAAAAAAaaaaaaaaaaaaaa on time

submitted 168 days ago • 1 comment

We start a new day of the Workshop on Genomics 2025 with the lecture on Genome Assembly by @camillemrcht.bsky.social and @npmalfoy.bsky.social! They always have a way to make the theory behind genome assembly enterntaining and exciting! 🤩 #evomics2025 #bioinformatics #genomics

submitted 169 days ago • 1 comment

We may have cut our last Canu release in 2024, but we are starting off 2025 with Verkko2! 🎉 Not only is it 4x faster than Verkko1, this version integrates Hi-C data for both phasing and scaffolding, enabling the automated assembly of acrocentric chromosomes! Preprint: www.biorxiv.org/content/10.1...

submitted 176 days ago • 5 comments

Glad to see metaMDBG in the line-up of assemblers 💚

submitted 176 days ago • 0 comments

Merry lexicographic minimiz... Christmas arxiv.org/abs/2412.17492

submitted 185 days ago • 0 comments

We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! github.com/bluenote-157... www.biorxiv.org/content/10.1... 1/5

submitted 191 days ago • 1 comment

🚨🚨🚨 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...

submitted 197 days ago • 1 comment

Glad to share our preprint 🏃 LongTrack: long read metagenomics-based precise tracking of bacterial strains (and their genomic changes!) after 💩 fecal microbiota transplantation. A 4+ years journey and tour de force by @yufan01.bsky.social & team. A long 🧵 www.biorxiv.org/content/10.1...

submitted 198 days ago • 2 comments

🚨You've got to read this one. 🚨

submitted 210 days ago • 0 comments

We are also blessed with cool metagenomic talks, @gaetanbenoit.bsky.social who presented a preview of his new nanopore metagenomoc assembler,

submitted 211 days ago • 1 comment

Hi Bluesky! Live from the Seqbim workshop, our yearly national workshop on sequence bioinformatics. We started with a strobecool keynote by @ksahlin.bsky.social ! He overviewed strobemers, and related developments.

submitted 211 days ago • 1 comment

Excited to join the #Nanopore Community on BlueSky. Follow us for the latest updates and discussions about Oxford Nanopore and Nanopore Community. #WYMM

submitted 217 days ago • 2 comments

Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla. doi.org/10.1101/2024... @wwood @rhysnewell @CMR_QUT 🧵1/6

submitted 213 days ago • 7 comments

🧬🔍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

submitted 228 days ago • 2 comments

Long-read special issue of GR is out, including our paper on T2T assembly using only Nanopore. Just in time for ONT to discontinue duplex cells on Nov 27 😅😂 Good thing Verkko also works great with HERRO-corrected simplex data! 📄 genome.cshlp.org/content/34/1... 📖 genome.cshlp.org/content/34/1...

submitted 218 days ago • 4 comments

I wrote about the backstory of our recently published metagenomic profiler called sylph (www.nature.com/articles/s41...), partially to celebrate the new migration to bluesky Check out the blog here: jim-shaw-bluenote.github.io/blog/2024/de... -- and I apologize in advance for the lack of brevity :)

submitted 220 days ago • 1 comment

Love this idea for helping the community make the transition to Bluesky, so I’ve compiled a woefully incomplete list of microbial ecologists and -omics peeps I know are here. Please make suggestions and share. Let me know if you’d like to be added. go.bsky.app/TQpaTqF

submitted 229 days ago • 77 comments

We finished yesterday’s #GenomeInformatics24 with @gaetanbenoit.bsky.social describing metagenome assembler MetaMDBG now for nanopore data NanoMDBG. Using chained minimisers, piled up to detect errors.

submitted 224 days ago • 0 comments

One more opening in my group at Oxford Nanopore. This time in our New York office! ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...

submitted 503 days ago • 0 comments

Very excited to see a new metagenome asssembly algorithm available for PacBio HiFi data! metaMDBG performs extremely well based on my benchmarks and we plan on using it for several deep-sequencing projects. doi.org/10.1038/s415...

submitted 539 days ago • 0 comments