iiinova — where your digital self keeps evolving

Wei Shen 沈伟 @shenwei356.bsky.social · 24/09/2026

SeqKit is now faster and uses 40% less memory when reading large FASTA records, such as human genomes, though it still uses more RAM than tools written in C/C++/Rust. Worth upgrading! github.com/shenwei356/s...

github.com

GitHub - shenwei356/seqkit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation - shenwei356/seqkit

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Wei Shen 沈伟 @shenwei356.bsky.social · 24/09/2026

csvtk brings several new commands and lots of new features! It's getting harder to find the time to meet all users' expectations (new features) without the help of AI agents. I hope these toolkits will remain useful and continue to benefit people in the AI era. github.com/shenwei356/c...

github.com

GitHub - shenwei356/csvtk: A cross-platform, efficient and practical CSV/TSV toolkit in Golang

A cross-platform, efficient and practical CSV/TSV toolkit in Golang - shenwei356/csvtk

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Heng Li @lh3lh3.bsky.social · 17/09/2026

Single-page, interactive overlap assembler for teaching purposes: lh3.github.io/teach-demo/o... (vibe coded)

lh3.github.io

Overlap Graph Assembly Demo

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Jim Shaw @jimshaw.bsky.social · 15/09/2026

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)

sylph-docs.github.io

Documentation for sylph - ultrafast, precise metagenomic profiling

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Zamin Iqbal @zaminiqbal.bsky.social · 09/09/2026

More than a decade since Mykrobe first came out - v happy @martibartfast.bsky.social has developed a Go version, which means we could revive the old app, which always made it much more accessible. Same results as Mykrobe but faster.

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Igor Martayan @imartayan.bsky.social · 04/09/2026

This is in 2 hours! In the meantime, you can look at the slides here: igor.martayan.org/slides-phd.pdf

igor.martayan.org

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Wei Shen 沈伟 @shenwei356.bsky.social · 03/09/2026

It's really a great opportunity!

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Wei Shen 沈伟 @shenwei356.bsky.social · 24/08/2026

Yeah, totally agree. The option needs to accept one or more paths as well. For system-level cleaning, it still requires root privileges, which are nearly impossible to obtain on clusters.

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Rob Patro @robp.bsky.social · 15/08/2026

Cuttlefish 3 is on bioconda! 🦑 A parallel, external-memory algorithm for building colored compacted de Bruijn graphs at collection scale — a RECOMB 2026 paper, and as of today a production release: v3.0.0. A thread on the algorithm, the numbers, and why the released tool is a Rust rewrite. 🧵 1/10

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Ryan Wick @rrwick.bsky.social · 24/07/2026

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

rrwick.github.io

Benchmark update: Ilesta, Autocycler-fast and new versions

a blog for miscellaneous bioinformatics stuff

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Zamin Iqbal @zaminiqbal.bsky.social · 25/06/2026

Honoured to be awarded the Mary Lyon medal by the Genetics Society today, here in Edinburgh. V grateful to mentors and all my previous group members and colleagues. Medal is an X chromosome!!

Gold/bronze coloured medal, with depicted X chromosome

Second side of medal says "Mary Lyon Medal" awarded to Prof Zam Iqbal. By the Genetics Society

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Daan Speth @daanspeth.bsky.social · 26/06/2026

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 🦠🖥️🧬

globdb.org

home | GlobDB

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 26/06/2026

2/2 ESA-E accepted: - SimdQuickHeap [w/ Johannes Breitling, Marvin Williams] - non-minimal k-PHF [Stefan Hermann, Peter Sanders, Stefan Walzer] and 2/2 WABI accepted: - O(n lg lg n) chaining [Nicola Rizzo] - anti-lex SUS-anchors arxiv: arxiv.org/search/?quer...

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Wei Shen 沈伟 @shenwei356.bsky.social · 24/06/2026

If I remember correctly, this is not the first project originally from your class! It must be very inspiring!👍

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Johanna von Wachsmann @johannavw.bsky.social · 16/06/2026

🧬 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...

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Heng Li @lh3lh3.bsky.social · 16/06/2026

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

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Kristian G. Andersen @kgandersen.bsky.social · 21/05/2026

Just a shout-out to the folks over at @pathoplexus.org and, importantly, all the scientists sharing genomic data with such amazing speed. It's great to see the field having moved to a new platform, with non-transparent platforms being a thing of the past. Fantastic.

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Igor Martayan @imartayan.bsky.social · 21/04/2026

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...

igor.martayan.org

Breaking ntHash (to better fix it)

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ace-gtdb.bsky.social @ace-gtdb.bsky.social · 15/04/2026

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.

gtdb.ecogenomic.org

GTDB - Genome Taxonomy Database

The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.

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LaurieWired @lauriewired.bsky.social · 07/04/2026

Modern DRAM is based on a brilliant design from IBM. But, we're still paying for a latency penalty that's existed since the 60s! In this video, I'm introducing my research project (Tailslayer) that immensely reduces p99.99 latency on traditional RAM!

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Wei Shen 沈伟 @shenwei356.bsky.social · 13/03/2026

LexicMap v0.9.0 has been released with - a few bug fixes: CIGAR, bitscore and evalue calculation. - new features: better support for big genomes like human. - a new command to convert output to SAM format github.com/shenwei356/L...

github.com

Release LexicMap v0.9.0 · shenwei356/LexicMap

v0.9.0 - 2026-03-13 New commands: lexicmap utils 2sam: Convert the default search output to SAM format (#26). Attention: This command requires search results generated by the current LexicMap ver...

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Wei Shen 沈伟 @shenwei356.bsky.social · 01/03/2026

Thank you! Its original goal was to help beginners do some simple but common tasks. Before that, I shared Perl and Python scripts to help students, but they struggled to install the Perl modules. At that time, Go 1.0 was released, with a great feature of easily providing executable binaries.

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Wei Shen 沈伟 @shenwei356.bsky.social · 27/02/2026

Thank you, James! Glad you like it.

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Wei Shen 沈伟 @shenwei356.bsky.social · 27/02/2026

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...

github.com

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....

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Zamin Iqbal @zaminiqbal.bsky.social · 26/02/2026

I should have said, this takes us to about 2.8 million genomes in total. We don't have annotations, etc for the latest data yet, this will be an ongoing process

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Zamin Iqbal @zaminiqbal.bsky.social · 09/02/2026

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)

nature.com

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.

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Wei Shen 沈伟 @shenwei356.bsky.social · 02/02/2026

> We will change several names that have long been in use (e.g., Firmicutes, Proteobacteria) to newly formalized names (e.g., Bacillota, Pseudomonadota) that may be unfamiliar to some. ncbiinsights.ncbi.nlm.nih.gov/2022/11/14/p...

ncbiinsights.ncbi.nlm.nih.gov

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Zamin Iqbal @zaminiqbal.bsky.social · 19/01/2026

For those of us interested in software development, data structure design etc in science, this is a must-read. A taste of what is happening in communities letting AI agents go wild writing code, creating PRs, writing documentation : spoiler - humans get addicted, lose perspective, slop everywhere.

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Wei Shen 沈伟 @shenwei356.bsky.social · 04/01/2026

Phage therapy of perinephric abscess in kidney transplantation recipients caused by drug‐resistant Pseudomonas aeruginosa - Liu - 2025 - mLife - Wiley Online Library onlinelibrary.wiley.com/doi/10.1002/...

onlinelibrary.wiley.com

Phage therapy of perinephric abscess in kidney transplantation recipients caused by drug‐resistant Pseudomonas aeruginosa

Click on the article title to read more.

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Qiyun Zhu @zhuqiyun.bsky.social · 11/12/2025

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

nature.com

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

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Wei Shen 沈伟 @shenwei356.bsky.social · 11/12/2025

So did I, but I'm serious this time.

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Wei Shen 沈伟 @shenwei356.bsky.social · 11/12/2025

Yes, finally! I bought the first Rust Book in 2019 ...

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Wei Shen 沈伟 @shenwei356.bsky.social · 11/12/2025

My first Rust toy tool (just for learning purposes)!!! The performance (both time and memory) is good! Rust is hard to learn, and I still need more practice! github.com/shenwei356/f...

Performance on reading and writing plain FASTA/Q files

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Zamin Iqbal @zaminiqbal.bsky.social · 20/11/2025

Most exciting study have seen for ages, and Fernando the most excited speaker. Much anticipated. Highly recommended, a lot of food for thought (and quite a dense paper - lots to think about)

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Microbiome Virtual International Forum @microbiomevif.bsky.social · 17/11/2025

It's Monday! ...and a new #MVIF program is out! 🤩 Free registration: cassyni.com/s/mvif-44 ⭐️ Highlights: 🇺🇸 Vanessa Hale 🇰🇷 Jun Hyung Cha ⭐️ Keynote: 🇺🇸 Katherine Lemon @kathlemon.bsky.social ⭐️ Talks: 🇺🇸 Meenakshi Chakraborty 🇨🇳 Wei Shen @shenwei356.bsky.social 🇺🇸 Johanna Gutleben

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Vivek Mutalik @vivekmutalik.bsky.social · 16/11/2025

📣 New preprint from us at phagefoundry.org 📣 A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort www.biorxiv.org/content/10.1...

phagefoundry.org

Phage Foundry

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Zamin Iqbal @zaminiqbal.bsky.social · 14/11/2025

Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.

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Camille Marchet ⚡ @camillemrcht.bsky.social · 06/11/2025

Thread on #GI2025 's second day! 👇🏻

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Sina Majidian @sinamajidian.bsky.social · 06/11/2025

Ben Langmead @benlangmead.bsky.social delivers the official opening for this year's Genome Informatics Conference #GI2025 at Cold Spring Harbor Laboratory. List of talks and posters: meetings.cshl.edu/abstracts.as...

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 04/11/2025

Cool paper new paper from Lorién López-Villellas, @santiagomarco.bsky.social and others! Super cute and simple idea: In Gotoh's affine-cost alignment, only the M matrix is needed during tracing: we can just search for a gap-length x such that M[i][j] = M[i-x][j]+o+x*e or M[i][j] = M[i][j-x]+o+x*e.

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Titus Brown @titus.idyll.org · 29/10/2025

I also have serious concerns about the consolidation of roles (one person is now publisher, chief editor, and also a frequent author) as exemplified in a recent paper that was fast-tracked for publication.

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 23/10/2025

Really exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.

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Rick Beeloo @rickbitloo.bsky.social · 23/10/2025

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

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Wei Shen 沈伟