Jim Shaw

Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....

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...

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...

Detecting foldback artifacts in long-reads - BMC Genomics Long-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of ...

Our paper on foldback artifacts in long-read sequencing is now published in BMC Genomics!

We introduce Breakinator to flag foldback and chimeric artifacts across library types, sequencers, and chemistries.

Paper: link.springer.com/article/10.1...

With Matthew Meyerson and @lh3lh3.bsky.social

Excited to share our latest work on early-life Bifidobacteria. We built a global genomic atlas of 4,000+ genomes from 48 countries for B. infantis and B. longum, expanding previous resources by 15-fold.

Read the press release @sangerinstitute.bsky.social: www.sanger.ac.uk/news_item/mi...

Were you aware that these are available for the community:
- an efficient fasta/q parser in Rust
- a quick rolling hash library
- a minimizer library
All in Rust 🦀

Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁

Great to see that Emu's still being worked on and updated!

Indeed, I think Emu and savont will serve different niches in the future and its very cool to see your development. Thanks for the informative post.

Recent updates Contribute to treangenlab/emu development by creating an account on GitHub.

I enjoyed reading your post @jimshaw.bsky.social and learning about Savont, thank you for the comparison to Emu and kudos on your new tool!

relevant to points raised in the post, the Emu development team has compiled our follow-up thoughts here: github.com/treangenlab/...

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

If you have an interest in mixing computation and experiments to understand microbial evolution (for example antibiotic resistance) and you think you might be a good fit for a postdoc in my lab, reach out. If it seems it might be a fit I’m happy to help you frame it as AI for Biology per this call

QuadRank: Engineering a High Throughput Rank Given a text, a query $\mathsf{rank}(q, c)$ counts the number of occurrences of character $c$ among the first $q$ characters of the text. Space-efficient methods to answer these rank queries form an i...

Now also on arxiv:
arxiv.org/abs/2602.04103

The online ANI calculator (skani) that allows you to compare your genome data with reference sequences in GTDB saves so much time and faffing around. :)

Thrilled to share our labor of love over the last 5 years 🤩

Leveraging long-read metagenomics (@nanoporetech.com) we identified some of the most prevalent gut phage families that have previously been overlooked in short-read based studies. [1/5]

Read more here: www.biorxiv.org/content/10.6...

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended our repository of available protein structures, ...

Multiple protein structure alignment at scale with FoldMason | Science https://www.science.org/doi/full/10.1126/science.ads6733?af=R

I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...

Awesome to hear, let me know how it goes.

Work supervised by @lh3lh3.bsky.social and in collab with @mkddueholm.bsky.social and his wonderful team.

Savont is still quite new, so feedback is more than welcome.

4/4

Using ASVs seems to avoid some issues with low-abundance, false-positive species calls from read mapping. Of course, ASVs will be less sensitive, though.

For more preliminary results and tests on actual data, see github.com/bluenote-157...

3/4

Preliminary: savont gets ASVs with ~10-30x less depth than previous denoising methods for *nanopore R10.4 amplicons*.

Essentially, previous short-read methods have difficulties with longer reads and higher error rates. Savont uses new techniques to handle this.

2/4

GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont

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...

New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued:
rrwick.github.io/2026/01/21/p...

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

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

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.

🎉 New year, NEW PREPRINT!

Bacteria exhibit astonishing genetic diversity, but where do new genes come from?

My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:

Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!

Release Version 0.17.0 · ksahlin/strobealign Changes #504: Introduce collinear chaining as the new default mapping and alignment method, replacing NAMs. This reproduces the Minimap2 chaining algorithm providing better mapping accuracy. NAMs ...

Strobealign v0.17.0 is out! github.com/ksahlin/stro...

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...