#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...

New blog post! I analyse the new [email protected] basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

Excited to have Alex Crits Christoph @acritschristoph.bsky.social join the lab today as a staff scientist! I had a hunch it was good time to find an experienced computational microbiologist to join the lab, but still feel very lucky to have him joining us. Looking forward to cool science!

Is @nanoporetech.com hac v6 better than 5.2.0 sup? The short answer is no. But are a few errors in a genome worth 5 times more basecalling compute? github.com/Kirk3gaard/M...

Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com​​​​​​​​​​​​​​​​ 🌐 https://search.foldseek.com/folddisco

Excited to share our review relating to the giant extrachromosomal elements (ECEs) We cover: why long-read metagenomics enables their discovery, genomic comparisons across recently characterized examples, and limitations of current classification tools. www.cell.com/trends/genet...

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

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...

Sensitive long-read amplicon sequence variant recovery with savont https://www.biorxiv.org/content/10.64898/2026.05.26.727271v1

Come to ONT's industry event at ASM to hear about two exciting new tools from @jimshaw.bsky.social! SNPmers (polymorphic kmers) are leveraged for impressive performance in both myloasm (metagenomic assembly) and savont (16S ASVs). Registration link 👇

Excited to speak at ASM Microbe 2026 in the Oxford Nanopore session about new tools for long-read metagenomics + 16S sequencing. If you're attending ASM Microbe June 4-7 in D.C. and want to chat, let me know!

TaxProfiler, the @nf-co.re #metagenomics pipeline had a new major release, adding multiple cool new classifiers (metacache, sylph and melon)! Great work by Sofia, @lilianderssonli.bsky.social , @jfy133.genomic.social.ap.brid.gy and others! 🙌 github.com/nf-core/taxp...

New versions of skDER (github.com/raufs/skDER) and zol (github.com/Kalan-Lab/zol) are now on Bioconda. Both have automated downloading of genomes based on species / genus name according to classifications in GTDB R232. The latest zol also incorporates FAMSA2 which provides considerable speed boosts!

Mushuvirus is the most widespread phage genus in the human gut. 🌍 Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi! How is it possible that they were hidden in previous metagenomic analyses? [1/7] Read: doi.org/10.64898/202...

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.

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_...

Great to see TRACS out in press - a new metagenomic strain transmission tool, led by @gerrythill.bsky.social. With improved precision and sensitivity, and unique support for custom reference and minor-strain detection, TRACS enables more rigorous and comprehensive strain-level metagenomics analysis.

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.

Finally out in @natmethods.nature.com 🎉 Our work with Wan Yue's lab shows that signal alignments from direct RNA @nanopore sequencing can reveal structural heterogeneity in RNA. Huge implications for RNA therapeutics! Read all about it here: www.nature.com/articles/s41...

Tiberius 2.0.0 is out 🎉 Now supports 7 eukaryotic clades, covering ~92% of NCBI assemblies. Modular rewrite + ~30% faster runtime. Benchmarks included, more soon. Thanks to Lars Gabriel, Richard Krieg & Felix Becker 🙌 github.com/Gaius-August... #bioinformatics #genomics #genomeannotation

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

Interested in a *staff computational scientist* position? We are looking for an experienced computational biologist (ideally with microbiology experience) to support published packages while also driving new research. Pay range $73k-$111k w excellent benefits. careers.peopleclick.com/careerscp/cl...

Friday was my last day at NHGRI. After 10 wonderful years, my lab is headed to Johns Hopkins University genomeinformatics.github.io/movingday/

Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

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...

This simulation-cum-benchmark study on MAG making by @tkorem.bsky.social & team looks really interesting. Loads of plots and results to work through! www.biorxiv.org/content/10.6...

Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added. 💾 github.com/steineggerla... 📄 doi.org/10.64898/2026.03.13.711249

With a 135 complete, circular Pelagibacter genomes, we have answered some of the most outstanding questions about what is often considered the most abundant organism on the planet, with roughly 10 million times more individuals in the ocean than stars in the universe. Check out our preprint.

Pelagibacter, resolved https://www.biorxiv.org/content/10.64898/2026.04.03.716430v1

Actinomarina, resolved https://www.biorxiv.org/content/10.64898/2026.04.03.716425v1

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/...

Want to annotate a bacterial genome with structures? @oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures www.biorxiv.org/content/10.6... #phagesky #microsky #microbiomesky

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!

Cenote-Taker 3's manuscript has now been reviewed and published in @peercomjournal.bsky.social ! 🎉 I love the mission and ethics of PCJ, focusing on rigorous peer review, open access, and author involvement in publishing. I highly recommend it to others! 🧬🖥️ peercommunityjournal.org/item/10.2407...

🧬 pathotypr is now on Bioconda! @pathogenomics.bsky.social conda install -c bioconda pathotypr Alignment-free lineage classification & drug resistance genotyping from WGS. Works with any pathogen bring your own SNP markers. ⚡ Rust, ~1s/sample 🖥️ CLI + GUI 🔗 github.com/PathoGenOmics-Lab/pathotypr

With myloasm (amazing work by @jimshaw.bsky.social @mgmarin.bsky.social @lh3lh3.bsky.social ), deeper sequencing, and VAE clustering, could we actually decompose a metagenome? I wouldn't say we completely decomposed the metagenome, but I think we've gotten further than nearly anyone else I know.

What happens when you use a strain-resolved assembler on 720 Gbp of Nanopore metagenome sequence? Simultaneous strain-level resolution of multiple co-occurring lineages from hundreds of single contig high-quality genomes, including 78 Pelagibacter. @tnn1.bsky.social and myself:

Studying DNA modification in microbes shouldn't be limited by methodology. 🧬 We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint: www.biorxiv.org/content/10.6...

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 run-length-compressed skiplist data structure for dynamic GBWTs supports time and space efficient pangenome operations over syncmers https://www.biorxiv.org/content/10.64898/2026.03.26.714584v1

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

Clustering proteins using DIAMOND is out now @natmethods.nature.com www.nature.com/articles/s41...

_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.

_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.

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.

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...

I just had that conversation earlier this week. The college dean is deciding if they will (dis)continue the bioinformatics training program for grad students. An argument for discontinuation is that students will use GenAI to help them code, so they don’t need to learn bioinformatics.

𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗮𝗻𝗱 𝗣𝗵𝗗 𝗽𝗼𝘀𝗶𝘁𝗶𝗼𝗻𝘀 𝗶𝗻 𝗖𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 / 𝗔𝗹𝗴𝗼𝗿𝗶𝘁𝗵𝗺𝗶𝗰 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 I am currently recruiting for both: 🔹 Postdoc position su.varbi.com/what:job/job... 🔹 PhD position su.varbi.com/en/what:job/... Please share with anyone who might be interested!