Roland Faure
@rfaure.bsky.social
Sequence bioinfomatician, algorithms, methods. Postdoc in Institut Pasteur in Rayan Chikhi's lab
When utilized in literature review, LLMs consistently 1. fail to mention female authors in female-led literatures, 2. insist that men are more influential or more heavily cited when this is contradicted by objective citation counts, and 3. attribute women’s work to hallucinated male scholars.
Glad to announce that our new long-read metagenomic SNP caller, SNooPy, is published in NAR! Existing long-read SNP callers are not designed for metagenomic data, check out our new solution 👉https://academic.oup.com/nar/article/54/10/gkag556/8700491 @narjournal.bsky.social
Min-frame transformation enables more sensitive viral genome alignment https://www.biorxiv.org/content/10.64898/2026.05.20.726535v1
This is now published in Genome Research (doi.org/10.1101/gr.2...). Thank you everyone for your feedback and also the anonymous reviewers who helped to greatly improve the paper. I hope this becomes a useful resource for the community.
Hash functions in nucleotide sequence analysis
Randomness is a powerful tool in the design and analysis of algorithms and data structures for nucleotide sequence data. Nucleotide sequences are not themselves random but are often randomized using hash functions. Despite their widespread use in genomics, there is no comprehensive review of the types of hash functions used and their various applications. In this survey intended for bioinformatic methods developers, we divide hash functions into four categories: scattering hash functions, permutations, minimum perfect hash functions, and locality-sensitive hash functions. For each category, we provide examples of both general-use hash functions that have been applied in nucleotide sequence analysis and hash functions that have been designed specifically for nucleotide sequence analysis. We highlight their salient properties, commonalities, differences, and application areas.
doi.org
1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.
New blog post! I use ntHash all the time to hash k-mers, yet it turns out it has some unexpected flaws (collision propagation, bias on leading zeros...). The good news: each of them can be fixed! igor.martayan.org/posts/breaki...
Breaking ntHash (to better fix it)
NtHash is a popular method for hashing k-mers in bioinformatics, yet it has some surprising flaws. In this post, I walk through a few of them, and show that they can arise naturally, without an advers...
igor.martayan.org
what's the current status of HERRO and (bacterial) nanopore? Last I saw was Ryan Wick's blog evaluating it. How many people now use it (or did it actually get folded into a basecaller, or did it get dropped in favour of something else)?
Super Bloom: Fast and precise filter for streaming k-mer queries https://www.biorxiv.org/content/10.64898/2026.03.17.712354v1
📌 Les #soumissions pour @jobim2026.bsky.social sont ouvertes jusqu'au 15/03/26. 📝 Soumission de travaux originaux, articles longs (+ PCI), activités de plateformes et de service, posters et démonstrations 📍 Plus d’infos sur : jobim2026.sfbi.fr #JOBIM2026 #bioinfo #Strasbourg
JOBIM 2026@jobim2026.bsky.social · 6mo ago📣 Ouverture des soumissionsSoumissions ouvertes pour #JOBIM2026 🎉 🗓️ 1er février → 15 mars 2026 👉 Posters, démos, highlights, articles longs, plateformes & services… 🔗 premc.org/jobim-2026/ #bioinfo #Strasbourg
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup. libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix github.com/ebiggers/lib...
GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate
github.com
"..based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes" from @martinsteinegger.bsky.social andco
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 8mo agoAccelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment https://www.biorxiv.org/content/10.64898/2025.12.17.694868v1
Inverted colored de Bruijn Graph for practical kmer sets storage https://www.biorxiv.org/content/10.64898/2025.12.08.692073v1
The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/
DSB 2026 Venice - February 18-19
Workshop Data Structures in Bioinformatics
dsb-meeting.github.io
1/9 Just out: k-mer indexes are the backbone of fast search in genomic data, but many degrade under small k, subsampling, or high diversity. With Ondřej Sladký and @pavelvesely.bsky.social we asked: can we build one that works efficiently for any k-mer set?
Bioinformatics Advances@bioinfoadv.bsky.social · 8mo ago🧮 Just out in Bioinformatics Advances: “FroM Superstring to Indexing: A space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)” Full article available: https://doi.org/10.1093/bioadv/vbaf290 Authors include: @pavelvesely.bsky.social, @brinda.eu
Preprint out! Check out our new long-read metagenomic SNP-caller, SNooPy 😀. Work with Chris Quince. Thread 🧵 👉 www.biorxiv.org/content/10.6...
Preprint Alert! We present new strategies to accelerate large-scale document comparison using MinHash-like sketches. A thread:
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 9mo agoCompressed inverted indexes for scalable sequence similarity https://www.biorxiv.org/content/10.1101/2025.11.21.689685v1
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...
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
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 11mo agoHigh-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
I am happy to share our new preprint introducing MADRe - a pipeline for Metagenomic Assembly-Driven Database Reduction, enabling accurate and computationally efficient strain-level metagenomic classification. 🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1 1/9
Starting #RECOMBseq with @rayanchikhi.bsky.social 's keynote. Here stressing our responsibility as scientists to enable access to a common good: genomic data
Side note: you could, speaking purely theoretically, also fit every microbe onto an SD card, which is within the weight limit for a carrier pigeon. For some distances, it would be faster than the internet for transmitting sequence libraries 7/
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
Michael Baym@baym.lol · last yr.Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/
Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them? If so, you might this little project: github.com/rrwick/conda...
GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions
a simple tool for listing conda environments with descriptions - rrwick/condaenvlist
github.com
So glad to have participated in #DSB2025, what a great workshop! For some mysterious reason it was the first time I attended after 3 years of sequence research. Thanks to all participants & organizers 😃
Ragnar's made some incredible optimizations on the computation of minimizers, can't wait to see how these improvements will benefit bioinfo tools!
Ragnar {Groot Koerkamp}@curiouscoding.nl · 2y agoNice result to end the day (night*): After discussions with @imartayan.bsky.social, the SIMD minimizer code now also does proper canonical (revcomp) minimizers: ~1ns/bp for fwd minis +0.4ns/bp with collect and dedup +0.6ns/bp with canonical hashes. Super happy how it's only 2x slower in the end!
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 🧬🖥️
So glad to have successfully defended my Ph.D. last week 😀 Work on producing haplotype-resolved metagenomic assemblies using noisy long reads (HairSplitter) and high-fidelity long reads (Alice assembler, unpublished yet). Thanks to my advisors Dominique Lavenier and Jean-François Flot ❤️
