Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv. Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen) github.com/bluenote-157... 1/6

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

Excited to speak at ASM Microbe 2026 in the Oxford Nanopore session about new tools for long-read metagenomics + 16S sequencing. If you're attending ASM Microbe June 4-7 in D.C. and want to chat, let me know!

Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...

Please share widely! We will imminently be posting a technician position in our lab group since @rheasood.bsky.social is off to grad school 🙌! If you know of anyone excited about molecular biology, evolution, and functional genomics please have them reach out (schumer at stanford). Start date ~June

Ver excited to share my just-published Darwin Review with @lh3lh3.bsky.social on population-scale long-read sequencing! royalsocietypublishing.org/rspb/article...

Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...

If you use fgbio or UMIs at all, you should start using fgumi. Up to 100x faster, and soon 2x faster sort than samtools, it’s been a labor of love and something we’ve wanted to do for a long time.

If you use our fgbio UMI tooling today, you owe it to yourself to check out fgumi! Massively faster re-write into Rust by @nilshomer.com with 100% reproduction of the fgbio outputs!

LongcallR for competitive SNP calling and haplotype phasing, and simplified allele-specific analysis with long RNA-seq reads. Found ~100 junctions affected by SNPs per sample with most junctions novel. Developed by Neng Huang. Published in @natmethods.nature.com. Read at rdcu.be/faKhL

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR

_720 Gbp_ marine nanopore metagenome -> 328 circular prokaryotic contigs: using myloasm! Insane work by Lui and Nielsen. Also shows how modern long read assemblies can disentangle coexisting strains and reveal ecological insights.

Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.

🚀 Hiring a Postdoc in Computational Genomics @ ETH Zurich Join the RADIANT-Dx project—a pioneering effort with UZH & University Hospital Zurich (with Ashley Rooney & Petra Dittrich)—to develop next-gen diagnostics using long-read sequencing & real-time analysis. 👉 www.jobs.ethz.ch/job/view/JOP...

𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗮𝗻𝗱 𝗣𝗵𝗗 𝗽𝗼𝘀𝗶𝘁𝗶𝗼𝗻𝘀 𝗶𝗻 𝗖𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 / 𝗔𝗹𝗴𝗼𝗿𝗶𝘁𝗵𝗺𝗶𝗰 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 I am currently recruiting for both: 🔹 Postdoc position su.varbi.com/what:job/job... 🔹 PhD position su.varbi.com/en/what:job/... Please share with anyone who might be interested!

🖥️ 🧬 ⚛️ 🔬 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!

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

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.

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

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

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

Now published in GigaScience with minor improvements: academic.oup.com/gigascience/... * Download: zenodo.org/records/1490... * More info: github.com/lh3/panmask

(Harvard STAT115): Introduction to Bioinformatics and Computational Biology by Shirley Liu. liulab-dfci.github.io/bioinfo-com...

Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar to SDUST but for long regions. github.com/lh3/longdust

Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

Neng Huang developed longcallR for joint SNP calling and phasing from long RNA-seq reads, AND for identifying allele-specific splicing/junctions (ASJ). Although ASJs of statistical significance are rare, a large fraction involve unannotated junctions. In Rust!

New metagenome assembler for ONT R10 and PacBio HiFi reads, from Jim Shaw. See Jim's thread for details

If you want to check if a human gene has copy-number changes or lands in a complex region, try pangene.bioinweb.org. Recently updated with more and better assemblies.

Posting on behalf of Shamil Sunyaev: Eimear(Vice Chair) and I (Chair) are organizing the 2025 Gordon Research Conference (GRC) on Human Genetics and Genomics, which will be held on July 6-11, 2025 in beautiful University of Southern Maine, Portland, Maine.

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

Minimap2-2.29 released with the support of short RNA-seq read alignment. More explanation and results here: lh3.github.io/2025/04/18/s...

Miniprot-0.15 released with minor improvement to alignment around tandem gene duplications. github.com/lh3/miniprot...

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...