🖥️ 🧬 ⚛️ 🔬 Plz spread the word. 2-week computational biology workshop in Singapore. No registration fee or expenses for US citizens. Protein annotation, function, structural modeling, and simulation. ~35 attendees. Lectures and hands-on tutorials with intensive instructor interaction. compbioasia.net
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
Pacific Biosciences Sells Short-Read Sequencing Assets to Illumina for $48.1M
www.pacb.com/press_releas...
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...
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!
Probably very minor
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.
Now published in gigascience: academic.oup.com/gigascience/.... Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.
To those who have open data at AWS cloud: you can use the S3 Bucket Browser to list files in your buckets. You can either 1) put the bucket name at lh3.github.io/s3bb/, 2) or copy this index.html github.com/lh3/s3bb/blo... to the root of a bucket. Generated by gemini.
Thanks to the AWS Open Data program, this dataset along some derived data is also openly accessible via @AWSCloud at openhgl.s3.us-east-1.amazonaws.com/index.html
Both SMEM and PML only use the rank operation, so yes, it should be easy to implement them in both tools. This just hasn't been done.
This plot compares SMEM from ropebwt3 and PML from movi. Ropebwt3 and movi don't support the same query type. It is hard to do an apple-to-apple comparison, but movi is indeed a lot faster.
The registration deadline is fast approaching for probgen 2026! Abstracts due by January 15, registration by January 31
probgen2026.github.io
I’m recruiting a postdoc to work on algorithms for cancer genome reconstruction. We have access to a rich set of tumour samples sequenced across multiple technologies. If interested, feel free to DM. Please share.
I guess there will be a version but probably not soon
579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm
📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI!
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
Back online. Not sure if it is a bug in my code or a hiccup at the hosting service.
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
arXiv accepted our assembly review two years ago. That was written in MS Word, so PDF-only. Nonetheless, at that time they didn't require TeX source as I remember. Something might have been changed internally.
And learn what fully AI-generated websites look like. Avoid them, as they are more likely to be scam.
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...
Now preprinted at arxiv.org/abs/2509.07357
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
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
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
Of course, also thank Andrea Guarracino and Andrew Carroll for their quick and careful review!
"Received: July 4, 2025. Revised: August 7, 2025. Accepted: August 15, 2025" and published on September 4. This is a simple and straightforward paper, but the speedy editorial process is still impressive. It could have been even faster if I had responded the initial editorial request more timely.
Now published in GigaScience with minor improvements: academic.oup.com/gigascience/...
* Download: zenodo.org/records/1490...
* More info: github.com/lh3/panmask
