Billy

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

Human de novo mutation rates from a four-generation pedigree reference - Nature Analysis of more than 95% of each diploid human genome of a four-generation, twenty-eight-member family using five complementary short-read and long-read sequencing technologies provides a truth set t...

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...

Complex structural variant visualization with SVTopo Structural variants are genomic variants that impact at least 50 nucleotides and can play major roles in diversity and human health. Many structural variants are complex multi-breakpoint rearrangement...

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 ✊

ESHG Conference 2025 ESHG 2022 COVID-19 Information Discover the ESHG 2025 - Hybrid Conference programme. We are proud to announce the confirmed 2025 speakers. Stay updated on matters related to the ESHG soc...

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.

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling AbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu

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

HiFi long-read genomes for difficult-to-detect, clinically relevant variants Clinical short-read exome and genome sequencing approaches have positively impacted diagnostic testing for rare diseases. Yet, technical limitations a…

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...

GitHub - PacificBiosciences/pb-StarPhase: A phase-aware pharmacogenomic diplotyper for PacBio datasets A phase-aware pharmacogenomic diplotyper for PacBio datasets - PacificBiosciences/pb-StarPhase

“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

Careers - PacBio PacBio is always looking to add the best and brightest minds to our world-class company. Our highly interdisciplinary team is best suited for individuals who are creative, forward thinking, and who ap...

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!

Binning meets taxonomy: TaxVAMB improves metagenome binning using bi-modal variational autoencoder A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. Currently, unsupervised and self-supervised deep learning based methods using co-abun...

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...

PacBio Announces SPRQ Chemistry for Revio Sequencing Systems, a Major Advance Reducing the Cost of a HiFi Human Genome to less than $500 - PacBio New long-read sequencing chemistry reduces DNA input requirements four-fold, enables a 33% increase in data output per SMRT Cell, improves methylation calling, and expands support for multiomics Trans...

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

Giulia Del Gobbo #ACMGMtg24 on lessons learned with Care4Rare using #PacBio #HiFi: need platform matched controls, discovering overlooked variants, phasing aid in interpretation, need specialized STR tools, and higher resolution of structural variants.

Emily Farrow #ACMGMtg24 on "Unveiling the power of #HiFi genome sequencing: one test to rule them all?" Clinical validation of #PacBio Revio; overall high validation accuracy; 26/50 cases with solves; average 25 day TAT; combination evaluation of SNV, CNV, SV, and methylation.

Release MethBat v0.9.0 · PacificBiosciences/MethBat Changes Adds a new segmentation mode based on Circular Binary Segmentation. This mode generates a BED file of methylated, unmethylated, and ASM regions. The mode is executed with methbat segment ....

We just added a methylation segmentation algorithm for PacBio HiFi data to our MethBat tooling (beta). If you are interested in trying it out, we would greatly appreciate any feedback on the performance and possible extensions!

Release here: github.com/PacificBiosc...

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...

Listening to _Four Thousand Weeks_ at 2x speed to save time.

With our outstanding partners at @GeneDx , @PacBio and @GoogleHealth, we will take on the biggest genomic diagnostic challenge of all, diagnosing rare diseases in individuals who are not only extensively tested already, but are from genetic ancestries ignored by medical genomics

Release HiPhase v1.0.0 · PacificBiosciences/HiPhase Changes Added support for tandem repeat calls from TRGT; minimum supported version - v0.5.0 VCF index files (.tbi) are now automatically generated by HiPhase The reference FASTA file is now a requ...

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...

GitHub - google/deepsomatic Contribute to google/deepsomatic development by creating an account on GitHub.

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...)

Release DeepVariant 1.6.0 · google/deepvariant Improved support for haploid regions, chrX and chY. Users can specify haploid regions with a flag. Updated case studies show usage and metrics. Added pangenome workflow (FASTQ-to-VCF mapping with V...

Release of DeepVariant v1.6.

Support for haploid regions, chrX/Y.
Workflow for Pangenome FASTQ-to-VCF.
Major DeepTrio improvements for de novo variants.
Models for CompleteGenomics T7, G400
Add NovaSeqX to training data

Release by Kishwar Shafin

github.com/google/deepv...