Jim Shaw

My thought on AI review: lh3.github.io/2026/10/27/l... TL;DR: journals are banning fully AI-generated review and I think that is the right decision

My final postdoc project is out today in Nature! We show microbes co-migrated with humans out of Africa; three independent methods agree, and timing matches archaeological / genetic evidence (Fig. 4c). Seeing Fig. 4c for 1st time was one of my most memorable "eureka" moments! doi.org/10.1038/s415...

Pleased to share my first preprint from my postdoc, where I ask what drives mobile DNA movement between bacterial cells in complex communities like the gut microbiome. To answer this, we built a way to capture mobile DNA in the act of moving between cells, using short-read metagenomics. 🧵

I’m excited to share our new preprint introducing HipHap, a tool for assigning long reads to haplotype-resolved diploid reference assemblies! With Max Marin, Matthew Meyerson, and @lh3lh3.bsky.social Preprint: www.biorxiv.org/content/10.6... 🧵 1/6

ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim 🐍pip install colabfold[alphafold] CF2 Sneak Peak with AF3/Boltz/Protenix/ESMFold2… 🐍pip install "colabfold[alphafold3]@git+https://github.com/sokrypton/ColabFold@af3-preview"

The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)

Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes: Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!). The manuscript was also published this summer in Genome Research! Links next...

Still relying on legacy approaches for microbial analysis? Join this webinar to discover the latest tools for resolving strain-level diversity, recovering complete genomes, and unlocking deeper insights from complex microbial communities. Register here: https://bit.ly/3UnBy0r

Glad to share StrainSpy, a new method developed by Sudaraka and co which identifies strain-level associations in metagenomics using ANI estimates from tools like Sylph. www.biorxiv.org/content/10.6...

Cool preprint about strain-level metagenome association studies using k-mer containment. Mallawaarachchi et al. from @gerrythill.bsky.social's group. I tried tackling this in our original paper for sylph (sylph-docs.github.io), but this seems to be much more sophisticated. Excited to read!

Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy https://www.biorxiv.org/content/10.64898/2026.08.30.748153v1

strobealign v0.18.0 is out, and it's now written in Rust. Handwritten by Marcel, started 2y ago. No LLM involved (yet*). Contributions by Nicolas and Ivan. 1/3

After a very long time, I'm very proud that we have now Joachim "magnus opum" on www.biorxiv.org/content/10.6... Protal is a ultra fast metagenomic species profiler. More precise than other profiled software, faster than most (not sylph though), but generates strain resolution instead.

Thank you for featuring our work National University Health System! Its great to have this article describe in simple terms what we have been doing for nearly a decade now in terms of microbial genomic surveillance and metagenomics 🥲 nuhsplus.edu.sg/article/dna-...

If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!

Travis has been cooking something up since IGGSy ;) A fast algorithm for SMEM finding in haplotype panels that uses space proportional to the number of 1s in the (sparse) matrix, inspired by the jump index [13].

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

The manuscript describing SimPhyNI is now published! www.microbiologyresearch.org/content/jour... A few updates since last post, including some method tweaks that improve performance and speed. Also even easier to run. Try it for your microbial GWAS or epistasis needs!

New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)

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...

Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!

1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools

minibwa-0.4 released with minor improvement and a few fixes to typos. Also a new blog post on "minibwa is the new bwa-mem": lh3.github.io/2026/07/04/m...

JOB ALERT! I'm hiring two postdocs in Computational Genomics to join our lab in beautiful Gothenburg, Sweden. Please share and repost! CGRLab.github.io/research/

Senior Bioinformatics Software Developer opening in my team in ONT's Applications department! Hybrid with a few days a week in our Oxford headquarters. We can sponsor visas! www.linkedin.com/jobs/view/44...

New study by Alexander Henoch (@ahenoch.bsky.social), a PhD student in our group @hifmb.de and @awi.de, shows what it takes to bring gene synteny into microbial pangenomes, and what we learn about the variability landscape of genomes when we do that. See the pre-print here: doi.org/10.64898/202...

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

I'm happy to announce the release of GlobDB r232! This version contains 346,233 bacterial and archaeal genomes, based on 26 datasets. More info globdb.org 🦠🖥️🧬

We're excited to share our work on how prophages influence the evolution of resistance against DNA-damaging antibiotics! This has been a fun project with @sianowen.bsky.social, @baym.lol, @theshreyaspai.bsky.social, @kepatitis-c.bsky.social, & @fernpizza.bsky.social biorxiv.org/content/10.6... 1/

Congratulations to my PhD student, Stefania Andrea Rosso Villanelo, on publishing her first first-author paper! 🎉In this study, she used antibiotics to facilitate the isolation of previously uncultured bacterial species from activated sludge. Check it out! 🦠🧫💊 journals.asm.org/doi/10.1128/...

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

🧬 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...

#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 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...

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...

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 👇