Antoine Limasset

Sora 2 Watermark Removers Flood the Web Bypassing Sora 2's rudimentary safety features is easy and experts worry it'll lead to a new era of scams and disinformation.

I think people are still unprepared for a world where you cannot trust any video content, despite years of warning.

Even when Google & OpenAI include watermarks, those can be easily removed, and open weights AI video models without guardrails are coming. www.404media.co/sora-2-water...

Burrows-Wheeler Indexing - YouTube Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

The Great Genotyper: a graph-based method for population genotyping of small and structural variants Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequenc...

A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."

"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary."
engineering.fb.com/2025/10/06/d...

A closed-loop method for precise genome size estimation using HiFi reads. #GenomeSize #HiFi #LongReads #Genomics #Bioinformatics #BMCgenomics 🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....

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 ...

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/...

We are alarmed by reports that Germany is on the verge of a catastrophic about-face, reversing its longstanding and principled opposition to the EU’s Chat Control proposal which, if passed, could spell the end of the right to privacy in Europe. signal.org/blog/pdfs/ge...

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching https://www.biorxiv.org/content/10.1101/2025.09.29.679204v1

#RECOMB2026 is now accepting submissions and we'd love to see your best work!

📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025

📜 More info: recomb.org/recomb2026/call_for_papers.html

I got my first "I object to you saying in class that there is no biological basis for a sex binary because the current political situation and also my religious views" email for the term.

Fun times.

Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin

What the heck is that ???????

Autocycler: long-read consensus assembly for bacterial genomes AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!

Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!

Les marchés publics de voyagistes - Contributions - 2025 - Aidez-nous à enrichir notre programme de travail - Plateforme de participation de la Cour des Comptes Corps de la contributionLes administrations et opérateurs publics, notamment ceux de l'enseignement supérieur et de la recherche, fond appel à des agences de voyage (FCM, TravelPlanet…) pour l'hôtelle...

Vous pouvez soutenir ma proposition à la Cour des Comptes d'examiner les marchés publics de voyagistes, notamment dans l'ESR :
participationcitoyenne.ccomptes.fr/processes/co...

Prière de soutenir cette demande (un compte est nécessaire, mais réalisable en 2min chrono, promis !) pour reconsidérer l'utilité des marchés voyages de nos institutions préférées.

Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

OYEZ!OYEZ!
Si vous avez des juicy stories d'agences de voyages de marché ESR avec des pratiques commerciales plus que douteuses, dites-moi en MP et je ferai passer à ma copine Orla.

Since errors are evaluated by aligning them to a reference, we can propose a new metric based on this alignment. This metric could evaluate the frequency of repeated errors at a given position and, more importantly, the deviation from the rate expected under a uniform distribution hypothesis.

Would an "imperfect" measure of uniformity be the proportion of errors that could be corrected at a given read depth using the given technology?

Thank you so much for the clarifications! I am indeed interested in the per-read accuracy, but I must admit I don't understand the importance of distinguishing between Ti and Tv.

This figure is extremely interesting, very surprising and exciting results from current state of sequencing technologies!

What a day for genome assembly!
Congrats to everyone!

Clinically routine T2T genomes are finally in sight! 🧪🧬💯 @genomeinabottle.bsky.social [14/14]

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

New blog post!

metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...

Both tools improved considerably! Time to update your conda environments 😄

64GB is definitely not enough

And MANY OOM...

How is dev going ?
WELL....