More and better human assemblies. Now annotate them to the minute. Special kudos @trhyker.bsky.social @jnalanko.bsky.social and @florisbarthel.bsky.social

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

🔍 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.

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

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_...

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:

Very excited for our lab's first paper to be printed!

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.

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...

Ver excited to share my just-published Darwin Review with @lh3lh3.bsky.social on population-scale long-read sequencing! royalsocietypublishing.org/rspb/article...

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...

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...

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...

This is from 7 years ago (merenlab.org/2019/02/24/f...). We are talking about the same things today. We will be talking about the same things 7 years from now. There is no one to blame for this apart from ourselves. I find it very depressing.

10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration www.nature.com/articles/s41...

Accepted to ISMB'26. Revised paper is here: jermp.github.io/assets/pdf/p.... I'd like to thank @robp.bsky.social once again and all the received feedback from the reviewers. To me, ISMB has had the highest quality review process over the past few years!

Whenever I presented Phold, I was frequently asked "can you do the same beyond phages?" We ( @oschwengers.bsky.social @linsalrob.bsky.social @binomicalabs.org et al) finally did it with Baktfold github.com/gbouras13/ba... www.biorxiv.org/content/10.6...

Following up on this - MADRe is now officially published 🎉 Very grateful for the guidance of @msikic.bsky.social @rvicedomini.bsky.social and Kresimir Krizanovic 🔗 academic.oup.com/gigascience/...

Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!

A run-length-compressed skiplist data structure for dynamic GBWTs supports time and space efficient pangenome operations over syncmers doi.org/10.64898/202...

LongcallR for competitive SNP calling and haplotype phasing, and simplified allele-specific analysis with long RNA-seq reads. Found ~100 junctions affected by SNPs per sample with most junctions novel. Developed by Neng Huang. Published in @natmethods.nature.com. Read at rdcu.be/faKhL

A quick rant on people vibe-translating our Rust libraries to other languages That's the second time in a week that I see new bioinformatics tools with a vibe-coded translation of our Rust libraries to C/C++. I have two major issues with that:

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

Preprint alert! TLDR: Super Bloom is a Bloom-filter variant for streaming k-mer queries. It uses minimizers to group adjacent k-mers into super-k-mers and map them to the same memory block. Result: much better locality, faster queries, and with the findere trick, dramatically fewer false positives.

How much protein diversity can Life on Earth actually generate? With DIAMOND DeepClust, we show how billions of proteins across the tree of life can be clustered at low-identity for downstream analytics tasks. 📚Paper: www.nature.com/articles/s41... 💻Code: github.com/bbuchfink/di...

_720 Gbp_ marine nanopore metagenome -> 328 circular prokaryotic contigs: using myloasm! Insane work by Lui and Nielsen. Also shows how modern long read assemblies can disentangle coexisting strains and reveal ecological insights.

Recently amplified gene arrays are a super interesting phenomenon, but many still resist our attempts to assemble them. @dantipov.bsky.social has developed a new method (Trivial Tangle Traverser) that resolves assembly graph tangles caused by such sequences (1/4) www.biorxiv.org/content/10.6...

Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.

Super Bloom: Fast and precise filter for streaming k-mer queries https://www.biorxiv.org/content/10.64898/2026.03.17.712354v1

It's a good day when the first item in your feed is your own work :) @rickbitloo.bsky.social was annoyed that scanning reads for all 96 rapid kit barcodes is bottleneck in Barbell, so he made Sassy2: 13x (150bp) to 4.6x (8kbp) faster than v1 by batch-searching patterns, and >100Gbp/s on 16 threads!

Very happy to share the latest paper of our group (et al.)! rdcu.be/e7zyX . This one has a special place… 1/n

1/ Our paper on Multi-Context Seeds is now out, with @tolyan.bsky.social spearheading the work and contributions from Nicolas and @marcelm.net. We introduce a new seeding concept that improves read alignment accuracy while maintaining speed. link.springer.com/article/10.1...

Can't wait to release a 10-year-old birthday version for SeqKit! - 10 years - 2 papers, 3500 citations - 20 contributors - 40 subcommands - 880 commits - 500 issues - 685.5K Bioconda total downloads Thank you all, dear contributors and users! I'll keep maintaining it. github.com/shenwei356/s...

How would you design a *multithreaded*, *concurrent* & *dynamic* hash table if you are focused specifically on common k-mer workloads, where streaming query & insertion are common? Jamshed, Prashant and I explore this in kache-hash, a cache-friendly k-mer hash table! www.biorxiv.org/content/10.6...

Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/ Bonus: beautiful seascape and friendly spirit!

Preprint alert! arxiv.org/abs/2602.03525 TLDR: ZOR filters are STATIC filters with false positives. -Almost memory optimal: <1% overhead over the theoretical lower bound (!!!) -Fast queries: ~100 ns -Construction cannot fail A thread:

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...

Announcing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...

Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster! www.biorxiv.org/content/10.6...

🗜️⚡ 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...

We just released #anvio v9, "eunice" 🎉 This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176. Read the release notes: github.com/merenlab/anv... Visit our up-to-date web page: anvio.org

Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.

Now published in Nature Biotechnology: go.nature.com/44P7nSm If you missed it, the TL;DR is in my April thread below

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

Preprint Alert! With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression! A thread:

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?

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 introduce new ideas to revisit the notion of sampling with window guarantees, also known as minimizers. A thread: