🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...

Excited to share our LongTrack study out in @natmicrobiol.nature.com today! Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/ 📄 rdcu.be/eL8mR

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...

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/...

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut. Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals. doi.org/10.1101/2025...

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

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV https://www.biorxiv.org/content/10.1101/2025.09.26.678787v1

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

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 😄

Many of the most complex and useful functions in biology emerge at the scale of whole genomes. Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

agtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀 • 11–24× fewer suboptimal alignments (same for human genome) • 3–579× lower inconsistency • improves on ~30% of reads aligned to non-target species github.com/mathjeff/map... bioconda.github.io/recipes/x-ma... #microsky

New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...

I sincerely appreciate the opportunity to visit @ebi.embl.org (thanks to the @embl.org Sabbatical fellowship). The guidance and support I received from Zam (@zaminiqbal.bsky.social), John (@bacpop.org) and other colleagues have been immensely valuable! You changed my career！❤️

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Now preprinted at arxiv.org/abs/2509.07357

How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1... Massive thanks to Klara for driving this

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

Check out Ryan's new blogpost, especially if you work on and polish small eukaryotic genome assemblies - it's always nice when someone adds new features for your tools

Now published in GigaScience with minor improvements: academic.oup.com/gigascience/... * Download: zenodo.org/records/1490... * More info: github.com/lh3/panmask

🌎👩‍🔬 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...

Our study developing a skin metatranscriptomics protocol is now out in @natbiotech.nature.com! We finally have the ability to study microbial activity on skin and identify key functional genes playing a role in diseases. Amazing team of Chia Minghao and Amanda Ng 👏 nature.com/articles/s41...

The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC rdcu.be/eCbj4

Thrilled to share our recent review on multidimensional metagenomics analysis, in which we highlight cutting edge technologies and AI applications at 1D to 4D levels. Congrats @hpeng.bsky.social and Angel Ruiz-Moreno. www.nature.com/articles/s44...

Our work on direct @nanoporetech.com sequencing of non-canonical bases in now out in @natcomms.nature.com! Read all about it here: nature.com/articles/s41... Great collab with Chew and Hirao lab x.com/NiranjanTW/s...

Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports... PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.

We are happy to announce that our latest manuscript has been published in Nature Communications! We identified the highly abundant and prevalent (>70% in population) giant (Max. 395kb) extrachromosomal element in the human mouth, named "Inocle". www.nature.com/articles/s41...

Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠 Proud to have contributed to Metalog, the latest @borklab.bsky.social resource: www.biorxiv.org/content/10.1... #microsky #microbiome

skani v0.3.0 is released. github.com/bluenote-157... - 30-40% potential reduction in memory with approximately the same runtime. - Breaking changes to indexing and searching databases Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.

taxburst v0.3.0 is now released - this is an update of the Krona visualization system for microbiome/metagenome taxonomy analyses. Enjoy!

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

Defining and cataloging variants in pangenome graphs https://www.biorxiv.org/content/10.1101/2025.08.04.668502v1

Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1

Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar to SDUST but for long regions. github.com/lh3/longdust

Synteny-aware functional annotation of bacteriophage genomes with Phynteny https://www.biorxiv.org/content/10.1101/2025.07.28.667340v1

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats www.nature.com/articles/s41... #jcampubs

High-throughput single-cell isolation of Bifidobacterium strains from the gut microbiome https://www.biorxiv.org/content/10.1101/2025.07.23.666462v1

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1... and GH repo: github.com/refresh-bio/...

We prepared an additional sylph database for the GlobDB with subsampling rate 1000 (-c 1000) requiring lower RAM than the default 200. Both databases and taxonomy are available at globdb.org

New sylph pre-built databases + taxonomy available for: - GTDB-R226 (143k prok. species) - GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social ) - UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social ) Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)

Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬

Detecting Foldback Artifacts in Long Reads https://www.biorxiv.org/content/10.1101/2025.07.15.664946v1

Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for next generation sequencing (pan)genome-resolved metagenomics and metatranscriptomics https://www.biorxiv.org/content/10.1101/2025.07.14.664802v1

Sassy is out now! Ever need to search for approximate matches of short DNA strings? Sassy is the tool to use! Available now wherever you get your code With @rickbitloo.bsky.social curiouscoding.nl/papers/sassy... github.com/ragnarGrootK...

Are you interested in microbes that are rare but active? We combined BONCAT with SIP and metaproteomics to improve the recovery of labeled proteins from such microbes. In this case, it illuminated a new anaerobic syntrophic acetate-oxidizing bacterium. tinyurl.com/a8j29dsr #microbiomesky #microsky

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - @benjwoodcroft.bsky.social go.nature.com/3IwOxHh

My colleague asked me to circulate this job posting for Professor / Associate Professor in Computational Biology / Genomics at the University of Tokyo (P.S. I'm not affiliated): www.k.u-tokyo.ac.jp/en/informati...

Great to see our manuscript on skDER & CiDDER - programs for selection of representative microbial genomes - now published. Please give them a try and if you have any feature requests or issues, just let us know. www.microbiologyresearch.org/content/jour... github.com/raufs/skDER

Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco