New preprint: Hunting for MSI in long-read data with Owl 🦉
Owl is an MSI caller purpose-built for #PacBio HiFi and integrated into our somatic workflow.
Data:
• Low baseline (~1–5%)
• 15–18% MSI-H instability
• Links GGAA repeats to EWS::FLI1 fusion
Preprint here: bit.ly/4beWECU
See you at P165 in 16 minutes. #ACMGmtg26
Happening today at 12:15 PM!
Join Matt Holt at #ACMGMtg26 for his talk on how #PacBio HiFi sequencing enables the discovery of pharmacogenomic haplotypes.
📍 Platform C
⏰ 12:15 PM
Not attending? Learn more about StarPhase for HiFi PGx in this explainer video: bit.ly/4b4ACUA
Rare Disease Month reminded us why we show up for families and the science driving answers.
We’re not stopping there. Pre-registration is open for Seq It Forward: Run for Rare 5K in June, supporting iHope and rare disease families.
Register: bit.ly/4u33kwB
#SeqItForward5K #PacBio #RareDisease #5K
Want epigenetic information automatically included in your sequencing runs?
HiFi sequencing detects 5mC and 6mA directly from native DNA and combines multiple passes of the same molecule to generate long reads with greater than 99.9% accuracy.
See how: bit.ly/3YSPBdo
#PacBio #HiFisequencing
HiFi sequencing can reveal rare and complex variants, but interpretation requires diverse background datasets.
PacBio and DNAstack are supporting the first global federated dataset of HiFi whole genomes through the HiFi Solves Global Consortium.
Details: bit.ly/4kQ0bMk
#WeCareForRare
By both improving accuracy and unifying assembly-based and mapping-based inferences, the portello approach has the potential to substantially improve analysis for rare-disease and other WGS applications. See our new preprint here:
doi.org/10.64898/202...
Comparison of read mappings at HG002 chr4:40,294,825-40,295,700, showing conventional (pbmm2) read mappings (above) and portello mappings (below). The same set of unaligned input reads were input into each mapping process.
What if you could improve small variant accuracy, CNV inference, and interpretability of your HiFi WGS data by taking a different approach to read mapping? Our new preprint describes portello, a method which demonstrates the potential for such improvements. (1/5)
You’ve heard the buzz around a more affordable long-read genome with SPRQ-Nx. Now we’re letting the data do the talking.
Newly published WGS datasets across human, plant, and animal genomes show you don’t need to compromise data quality for affordability.
Explore the data: bit.ly/3O7BAGv
#PacBio
A first in human genomics: a 4-generation pedigree reference, now in Nature.
Built with #PacBio HiFi, it maps de novo mutation rates, reveals paternal bias, and captures high mutation rates in tandem repeats—even in Y and repeat-rich regions.
Paper here: go.nature.com/4lGMPlP
#TheresHiFiForThat
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...
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:
For starters, the software carpentry lesson (swcarpentry.github.io/git-novice/) is pretty good. When things go wrong, or when you want to dig deeper, I like ohshitgit.com, and more generally, blog posts by Julia Evans related to git: jvns.ca#git
7500 research staff at the University of California filed a petition to form a union with UAW today at the Public Employment Relations Board in Oakland. While the work is really just beginning, we have had thousands of conversations to get here. We're going to win ✊
Also worth noting that a substantial new sawfish CNV integration feature will be coming as a preview release on GitHub later this month, which I’ll also be detailing as a poster presentation at ESHG. Looking forward to sharing more about this soon.
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...
Get in Dorks, we are going protesting.
STAND UP FOR SCIENCE. MARCH 7th 12-4pm. DC AND YOUR STATE CAPITALS.
More information to come.
Long-read sequencing resolves the clinically relevant CYP21A2 locus, supporting a new clinical test for Congenital Adrenal Hyperplasia https://www.medrxiv.org/content/10.1101/2025.02.07.25321404v1
Have a look at our latest work on PacBio LRS showing its potential as a single technology to accurately identify all types of clinically relevant variants.
www.sciencedirect.com/science/arti...
“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...
ICYMI my poster at #AMPath24, I'm sharing it here. Folks interested in long reads to resolve complex loci like repeat expansions relevant to neuro disease and carrier screening, check it out! @pacbio.bsky.social collab with @egor-dolzhenko.bsky.social @guilhermesena1.bsky.social and many others
@sedlazeck.bsky.social AMPath24 talk about long reads highlighting TRGT tool by @egor-dolzhenko.bsky.social and @guilhermesena1.bsky.social and others for HiFi sequencing by @pacbio.bsky.social
If you are a #C++ developer, either have a #bioinformatics or #CUDA background, and take pride in your engineering and/or algorithmic skills, I'm looking for a Senior Staff Engineer at @pacbio.bsky.social. You can work remotely. Feel free to ping me or go to pacb.com/careers
Please spread the word
We can see there's already excitement for Vega on Bluesky. ✨ What do you think about the first #PacBio HiFi benchtop system?
I think I'll try hiring @pacbio.bsky.social a #bioinformatics engineer with modern C++ skills. Interested? You can be remote in the US, UK, Germany, or Switzerland. Goals: implement crazy algorithms for on-instrument sequence data processing and improve existing solutions. Contact me.Spread the word
Waking up in my own normal body and freaking out like the guy who woke up as a bug
My poster on long read pharmacogenomics with #PacBio HiFi is up for today at #ASHG24. Ping me on here if you want to meet before the poster session!
A new #metagenomic binning algorithm has appeared: TaxVAMB
Looks like it may outperform SemiBin2 for @PacBio HiFi datasets (human gut). I use the long-read mode of SemiBin2 in the HiFi-MAG-Pipeline and it works great. Time to run some benchmarks!
www.biorxiv.org/content/10.1...
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...
Interested in long-read pharmacogenomics? Then I have some exciting things to show you at #ASHG24... Looking forward to next week in Denver!
#PacBio #PGx
