New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut. Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals. doi.org/10.1101/2025...

I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months! Aardvark: Sifting through differences in a mound of variants GitHub: github.com/PacificBiosc... Some highlights in this thread: 1/N

In Stockholm for work and got a great recommendation to Klättercentret Telefonplan for a boulder break last night. Great gym all around and easy hop on the metro from city center.

Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...

Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....

Very excited to share I’ll be starting my own group at University of Utah in the Department of Human Genetics in the new year! Reach out if you are interested! vollgerlab.com

Great keynote talk at #SFAF by Rob Knight, summarizing key innovations in microbiome research over the past decade. One recent highlight is how long reads have transformed metagenome assembly, particularly #PacBio HiFi reads. The future is complete MAGs!

Just released a major update to the sawfish SV caller, which adds CNV calling and integration. Assessment on a set of pathogenic CNVs from Gross et al. shows this integrated-call strategy can substantially improve (single-method) recall, especially at lower HiFi sequencing depths

Long-read sequencing of large pedigrees is an ideal way to map all classes of denovo mutations! A collaboration between University of Utah, University of Washington, and PacBio. Glad to be a part of this project 👏 www.nature.com/articles/s41...

This example is hard to understand from e.g. IGV/Ribbon (see Fig1) but pretty simple in SVTopo: 4 blocks deleted (B,D,F,H), 2 inverted (E,G), 1 re-ordered (C)

I just released a new preprint! The manuscript describes SVTopo, a software tool that enhances visualization of complex SVs using HiFi data: www.biorxiv.org/content/10.1.... Here’s a summary of the results:

Last day to submit abstracts to #HiTSeq25 @hitseq.bsky.social #ISMB2025 - send us your work for an opportunity to present in the podium or poster.

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/PacificBiosc...

Hello bluesky world! Newbee here! I have a postdoc position immediately available in my lab. It will focus on identifying high-quality transposons in many genomes and finding their impacts in evolution and traits. Most works, including EDTA2 development and annotation of 400+ genomes, are done! 1/n

🚀 Truvari v5.0 is here! 🎉 What’s new? 🔹 Enhanced symbolic variant support for <DEL>, <DUP>, <INV> 🔹 Robust BND comparison for cross-representation SV matching 🔹 Improved SV sequence similarity & HUGE SV support 🔹 Cleaner UI & Revamped API 👉 More: github.com/ACEnglish/tr... #Genomics #Bioinformatics

Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n) doi.org/10.1093/bioi...

Very excited to see this study out in the world. We made what is (we think?) the first fully-humanized mouse model of a repeat expansion disorder, DRPLA, by replacing an entire copy of muring Atn1 with human ATN1 with 112 pure CAG repeats... www.biorxiv.org/content/10.1...

Xiao Chen #ACMGMtg25 describing Kivvi tool for assembling long repeat units in medically relevant genes (KIV2 and D4Z4) using #PacBio HiFi reads. Large repeats accurately assembled!

My very first post on Bluesky Happy to be here. Check out our collaborative study with Bob Darnell @darnelr.bsky.social, where mice humanized for a NOVA1 gene variant unique to humans, produce more varied and complex vocalizations: www.science.org/content/arti... www.nature.com/articles/s41...

Excited to announce our preprint describing SUPERB-SEQ 🦸, a new method to measure Cas9 edits and their effects on gene expression in single cells. Led by @micklorenzini.bsky.social and @bradbalderson.bsky.social www.biorxiv.org/content/10.1...

EXTREMELY cool and demonstrates clearly the promise of deep learning + bio. www.nature.com/articles/s41...

“StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data” is now on biorxiv! In this work, we explore the use of long-read sequencing (#PacBio #HiFi) for #pharmacogenomics #PGx. 1/N Pre-print: doi.org/10.1101/2024... Repo: github.com/PacificBiosc...

The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics

Looking forward to some great talks at #ASHG24 in Denver this week. I’ll be there through Sat, supporting a poster on current/upcoming sawfish SV caller features (github.com/PacificBiosc...), and discussing other HiFi secondary analysis solutions. DMs are open if you'd like to sync up or hear more.

The new #PacBio SPRQ chemistry for the Revio system has some big advantages for micro and #metagenomics: - Input requirements drop from 2 micrograms to 500 nanograms (per SMRT cell) - 30% increase yield per cell (~90Gb -> 120Gb) www.pacb.com/press_releas...

Excited to announce that our accompanying paper on HiPhase has been published today, I'll highlight some of the additions in this thread! #PacBio #HiFi “HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing”: doi.org/10.1093/bioi...

I'm pleased to announce the release of HiPhase v1.0.0!  In addition to phasing small and structural variants from #PacBio #HiFi datasets, HiPhase now also includes support for phasing short tandem repeats (#STR) at the same time!   Full release notes can be found here: github.com/PacificBiosc...

Initial release of DeepSomatic, which identifies subclonal variants when given tumor and normal BAM files. Pre-trained models and case studies available for Illumina and PacBio. Development led by Kishwar Shafin which built off a framework by Pi-Chuan Chang. (github.com/google/deeps...)

Today we announce the first release of Severus: a new tool for somatic SV calling for long reads! It's designed for complex (and simple) rearrangements in cancer genomes, but also works well for germline github.com/KolmogorovLa...