Our method for genome size estimation from long-read overlaps is now published 🥳 academic.oup.com/bioinformati...

Thread on #GI2025 's second day! 👇🏻

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...

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.

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.

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.

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...

1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...

Podcast with me and @turiking.bsky.social for the @milnerevolution.bsky.social series, on plasmid evolution over the last 100 years, talking about our ( @cazares-adr.bsky.social , Nick Thomson, @sarah1alexander.bsky.social & co) recent paper www.science.org/doi/10.1126/... youtu.be/Mzr3TD4ijs0?...

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

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 tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)

Efficient and accurate search in petabase-scale sequence repositories www.nature.com/articles/s41... 🧬🖥️🧪 MetaGraph: metagraph.ethz.ch Code: github.com/ratschlab/me...

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

There are millions of openly available microbial genomes, but searching them can be slow. Until now 🥁 Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more. www.ebi.ac.uk/about/news/r... 🦠

Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

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

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - @shenwei356.bsky.social @zaminiqbal.bsky.social go.nature.com/3K09TgJ

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！❤️

Hashing vs. sorting; interesting! reiner.org/hashed-sorting. Also I wonder if, depending on your use case, semi-sorting provides an even greater benefit? 🧬🖥️

Amazing Jim!

Ok this is mad "...an ant that lays individuals from two distinct species. In this life cycle, females must clone males of another species because they require their sperm to produce the worker caste" www.nature.com/articles/s41...

🌎👩‍🔬 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...

Finally printed and submitted my thesis :) You may call me Dr. now 🎓 curiouscoding.nl/thesis.pdf

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

TaxonKit v0.20.0 is adapted to recent rank changes in NCBI Taxonomy. github.com/shenwei356/t... Also updated - taxid-changelog to May, 2025 github.com/shenwei356/t... - gtdb-taxdump to GTDB r226 github.com/shenwei356/g... - ictv-taxdump to VMR_MSL40 github.com/shenwei356/i...

⚡️LexicMap v0.7.0 fixed a minor bug in index building and improved the alignment accuracy! Please rebuild the existing index. Sorry for the inconvenience. 🥹 github.com/shenwei356/L...

🚀 ​LexicMap v0.6.0 is released! ✅ ​More accurate alignments! 🎯 ​Higher sensitivity for short queries (>100bp)! 💡 ​Denser seeds, same index size! 🔬 Function: Efficient sequence alignment against millions of prokaryotic genomes! 📖 Docs: bioinf.shenwei.me/LexicMap/

Thrilled to finally debut my lab site🎉: mbio.info — which stands for Microbial Bioinformatics, a domain I purchased 9 years ago and has been waiting for this moment ever since!"

Just updated seqkit, csvtk, taxonkit, and rush. Click to see changes: - github.com/shenwei356/s... - github.com/shenwei356/t... - github.com/shenwei356/c... - github.com/shenwei356/r...

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)

We're thrilled to introduce LexicMap v0.5.0🎉 It's more accurate and slightly faster! LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes! We'll provide an index for ATB on AWS later. github.com/shenwei356/L...

The story behind Sylph, from @jimshaw.bsky.social . It's quite inspiring to read. jim-shaw-bluenote.github.io/blog/2024/de...

We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! github.com/bluenote-157... www.biorxiv.org/content/10.1... 1/5

Strobealign v0.15.0 is released: (1) Allows more indexed contigs (2^32), (2) adds a mode --mcs which increase accuracy (paper on mcs www.biorxiv.org/content/10.1...). --mcs is still non-default in this release until we optimize it a bit more. Full changelog here github.com/ksahlin/stro...

🚨You've got to read this one. 🚨

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io

Bactopia now supports AllTheBacteria assemblies! If you are planning secondary analyses, this feature allows you to seamlessly use Bactopia. To demonstrate this, here's a blog post using Bactopia to analyze 5400 L. pneumophila assemblies bactopia.github.io/latest/blog/...

csvtk users, if you use `filter2/mutate2/mutate3` a lot like me, please update it to v0.31.1. I've fixed the slow speed since v0.27.0 (Aug 2023)😅. Conda-forge and Bioconda are not synced now. please download the binaries from GitHub. github.com/shenwei356/c...

Just updated taxid-changelog. Now you can track each NCBI Taxonomy taxon's detailed changes in the past 10 years😮😱😃 This is the proudest work I've done in my past 10+ year academic career, cause it's useful and funny but no one else did this, haha. github.com/shenwei356/t...

Align to AllTheBacteria with low RAM (1-2Gb) and quickly (seconds if just 1000s of hits, 15 mins for a gene present in all 2.4 million genomes) using @shenwei356.bsky.social Lexicmap. So you can basically BLAST AllTheBacteria locally - but need 3-4Tb disk for index www.biorxiv.org/content/10.1...

Is everyone moving to blue sky?

I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq

I'm going to be advertising a PhD studentship (open to international students) working on long read pangenome / assembly algorithms in bacteria. Would suit someone with maths/compsci background. Aptitude and interest more important than experience. Do please spread the word. Advert to follow

Great pleasure to work with Wei Shen on a new indexing and alignment scheme, called LexicMap: www.biorxiv.org/content/10.1... We have been working on uniformly reassembling, QC-ing and annotating all bacterial (and now archaeal) data, and we wanted to be able to do full alignment to it....