Notable finding #1: the current version of metaMDBG is quite good! Fast, very memory efficient and now one of the most accurate assemblers. Nice work, @gaetanbenoit.bsky.social! github.com/GaetanBenoit... (2/3)
Gaëtan Benoit
@gaetanbenoit.bsky.social
Postdoc researcher in bioinformatics at Pasteur institute. Scalable methods and software for metagenomics. https://github.com/GaetanBenoitDev
New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)
Benchmark update: Ilesta, Autocycler-fast and new versions
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...
The planktonic microbiome of the Great Barrier Reef - Nature
The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...
nature.com
Lossless compression of k-mer matrices enabling random row access https://www.biorxiv.org/content/10.64898/2026.07.03.736306v1
Follow-up to my last blog post: I now look at assembly polishing with Dorado v2 and the new hac@v6.0.0 model from @nanoporetech.com. rrwick.github.io/2026/06/19/d...
Dorado v2.0.0 part 2: assembly polishing
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
Just submitted my PhD thesis on algorithms for fast, large-scale k-mer-based sequence analysis. It's now available to read at phd.martayan.org Take a look and feel free to share! #Bioinformatics #PhDone
Algorithm design and implementation for the scale of sequencing data
phd.martayan.org
New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...
Dorado v2.0.0: no more sup?
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12
Thought i'd highlight that the ONT London Calling tech talk is now up. Points of interest for the microbiome community: 1) Direct RNA multiplexing now available. Can now run 24 samples per flow cell, recover full-length transcripts with 8 base pair modifications... www.youtube.com/watch?v=CE69...
London Calling 2026 Technology update
YouTube video by Oxford Nanopore Technologies
youtube.com
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
Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv. Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen) github.com/bluenote-157... 1/6
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2mo agoSensitive long-read amplicon sequence variant recovery with savont https://www.biorxiv.org/content/10.64898/2026.05.26.727271v1
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...
biorxiv.org
Fast Set Operations for Compact k-mer Sets https://www.biorxiv.org/content/10.64898/2026.05.24.727514v1
More and better human assemblies. Now annotate them to the minute. Special kudos @trhyker.bsky.social @jnalanko.bsky.social and @florisbarthel.bsky.social
Floris Barthel@florisbarthel.bsky.social · 3mo agoThe human genome's most variable and clinically important regions (centromeres, telomeres, and acrocentric short arms) have been hardest to study at scale. Thrilled to share KaryoScope, our new preprint that brings them within reach. 🧵 www.biorxiv.org/content/10.6...
Note that I released a new version of metaMDBG (v1.4) last week focusing on scalability. You can now process such dataset in 6 days and 130 GB of memory
Christine He@christinehe.bsky.social · 3mo agoReleased today: ~1.5 Tbp of ONT metagenomic sequencing from compost. Assembly, MAGs, and downstream analysis are available to play with epi2me.nanoporetech.com/compost_mgx_...
🔍 New paper in Bioinformatics Advances: "Kaminari: A frugal colored index for approximate k-mer queries" Read it here: https://doi.org/10.1093/bioadv/vbag120 Authors include: @yhhshb.bsky.social, @yoann.bsky.social, @robp.bsky.social, @pierrepeterlongo.bsky.social, @jermp.bsky.social
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
PPaul Medvedev @pashadag.bsky.social · last yr.
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.
The RECOMB-Seq 2026 program is now available! Join us May 24–25 in Thessaloniki, Greece, for two days of cutting-edge biological sequence analysis, with keynotes by Camille Marchet (CNRS) and Manolis Kellis (MIT). Full schedule: recomb-seq.github.io/seq2026/prog... #RECOMBseq
Program
RECOMB-Seq 2026 Web Page
recomb-seq.github.io
Released today: ~1.5 Tbp of ONT metagenomic sequencing from compost. Assembly, MAGs, and downstream analysis are available to play with epi2me.nanoporetech.com/compost_mgx_...
Metagenomic Assembly Sheds Light on Microbial Diversity in Compost
Overview We are pleased to release a metagenomic dataset from deep sequencing of a mature compost…
epi2me.nanoporetech.com
New preprint: The SimdQuickHeap is the fastest priority queue by far! 2x faster than a radix heap and up to 10x faster than binary heaps. arxiv.org/abs/2604.25681 with Marvin Williams and Johannes Breitling:
SimdQuickHeap: The QuickHeap Reconsidered
Priority queues are data structures that maintain a dynamic collection of elements and allow inserting new elements and removing the smallest element. The most widely known and used priority queue is ...
arxiv.org
Very excited for our lab's first paper to be printed!
Nucleic Acids Research@narjournal.bsky.social · 3mo ago⭐ #NARBreakthrough ⭐ New study delivers the first chromosome-level phased assemblies, uncovering >50,000 #structuralvariants and rescuing millions of #unmappable reads in BJ and IMR-90 human cell lines. 📖 Read here: doi.org/10.1093/nar/... #Genomics #CellLines #CommunityResource
HERRO has been published in @nature.com nature.com/articles/s41.... This achievement is a result of the great work by Dominik Stanojevic, with contributions from Dehui Lin, @sergeynurk.bsky.social, and Paola Florez de Sessions Welcome to the era of high-quality genome assemblies supported by AI.
Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads - Nature
Nature - Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads
nature.com
Excited to finally share our new preprint on bioRxiv describing Verticall (github.com/rrwick/Verti...), a robust & efficient tool for building recombination-free bacterial phylogenies. Huge thanks to @rrwick.bsky.social & @katholt.bsky.social for this incredible work! www.biorxiv.org/content/10.6...
biorxiv.org
Ver excited to share my just-published Darwin Review with @lh3lh3.bsky.social on population-scale long-read sequencing! royalsocietypublishing.org/rspb/article...
Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics
Abstract. Population-scale long-read DNA sequencing (PLRS) is rapidly reshaping our understanding of genomic variation in humans and non-model species. In
royalsocietypublishing.org
Turns out that the usual NtHash is not as random as one might think?!?! At least not for minimizers. Seq-hash (and simd-minimizers) already has this fixed by default ;) github.com/rust-seq/seq...
Igor Martayan@imartayan.bsky.social · 4mo agoNew 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...
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
I was investigating the genomes that I didn't manage to convert to near-complete MAGs in my assembly graph (the components in gray). The circle on top left is actually a complete genome but with 40% completeness (both in metaMDBG and myloasm)
Two more days to submit your abstract for a short talk or poster at RECOMB-Seq 2026. See instructions at recomb-seq.github.io/seq2026/call...
