GitHub - PacificBiosciences/Paraviewer Contribute to PacificBiosciences/Paraviewer development by creating an account on GitHub.

My new tool Paraviewer is now available for use at github.com/PacificBiosc...! If you use Paraphase, try this new next-step tool - it automates and greatly simplifies variant visualization from Paraphase variant calling. If you're at #ASHG2025, visit me today at poster 4109W. #pacbio

#PacBio announces major upcoming advances for #Revio and #Vega designed to lower genome costs, expand multiomic capabilities, and support regulated research.

The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.

View the press release: bit.ly/4o06eyH

Complex structural variant visualization with SVTopo - BMC Genomics Background Structural variants are genomic variants that impact at least 50 nucleotides. Structural variants can play major roles in diversity and human health. Many structural variants are difficult to interpret and understand with existing visualization tools, especially when comprised of inverted sequences or multiple breakend pairs. Results We present SVTopo, a tool to visualize germline structural variants with supporting evidence from high-accuracy long reads in easily understood figures. We include examples of 101 visually complex structural variants from seven unrelated human genomes, manually assigned to ten categories. These demonstrate a broad spectrum of rearrangement and showcase the frequency of complex structural variants in human genomes. Conclusions SVTopo shows breakpoint evidence in ways that aid reasoning about the impact of multi-breakpoint rearrangements. The images created aid human reasoning about the result of structural variation on gene and regulatory regions.

My complex variant visualization tool SVTopo is now officially published in BMC Genomics! link.springer.com/article/10.1.... This tool allows HiFi users to view complex germline structural variation in intuitive and informative plots.

It absolutely warms my heart when I click on a pre-print that includes a bunch of top methods folks from industry and I see (1) open-source software (with a good license; MIT in this case) that is (2) written in Rust. Bravo @pacbio.bsky.social!

Moar Rust plz!

github.com/PacificBiosc...

Arthur continues, showcasing how long-read sequencing discovered a novel fusion in an ovarian cancer patient—one that short-read methods miscalled as simple overexpression of the 3' fusion partner. #AACR25 #PacBio 

Interesting work from Khi Pin Chua, PhD on precise characterization of complex repeat regions in cancer genomes at #AACR25. Catch him at poster 2 in section 46 (#6288) until 5 PM! #PacBio

4 generations help science explore genome mutation rate - UW Medicine | Newsroom

Advanced genomic analysis of 4 generation family offers new knowledge about genetic mutations & their transmission, including inherited variants & those that arise anew
@nature.com @uwgenome.bsky.social @eichlerlab.bsky.social @uwmedicine.bsky.social @utah.edu @pacbio.bsky.social

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...

Really neat paper out, using measurements of 3D genome folding (with our Proximo Hi-C tech, wink wink) to pinpoint the CA2 gene as a potential target to reverse drug resistance in #breastcancer.

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:

Fusion transcript plot

Checkout out a new release of pbfusion (0.5.0) for accurate detection and visualization of fusion transcripts from @pacbio.bsky.social HiFi data.

github.com/PacificBiosc...

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...

Plots of SNP and Indel error numbers for DeepVariant models. Shows a Indel error reduction of 26% for PacBio and a ~50% SNP error reduction for ONT.

Added SPRQ to PacBio training, reducing Indel error on SPRQ by 26%. Added Platinum Pedigree training data for PacBio model, reducing errors by 34% on more extensive Platinum truth. New model and case study for Kinnex/Mas-Seq/Iso-Seq. Additional speed options for GPU pipelines 2/3

Runtime figure for new version of DeepVariant with and without small model. Showing reduction in runtime of 155 minutes to 101 minutes with Illumina, 174 minutes to 71 minutes with PacBio, and 295 minutes to 114 minutes with Oxford Nanopore.

Release of DeepVariant 1.8. Large speed improvement (~67% faster) via small model for easy sites. New Pangenome-aware option. Reduces error by ~30% for vg-mapped WGS, ~10% for BWA WGS, ~5% BWA exome. New config for custom model users, see release notes.

(github.com/google/deepv...)

Our special issue @genomeresearch.bsky.social is out on long-read sequencing (@pacbio.bsky.social & ONT): genome.cshlp.org/content/34/1...

Super excited about all the new work and special thanks to all the authors! Big thanks to Hillary @ahoischen.bsky.social @anaconesa.bsky.social

Howdy, please add me. All things genomics 😊

Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data Variant calling using long-read RNA sequencing (lrRNA-seq) can be applied to diverse tasks, such as capturing full-length isoforms and gene expression profiling. It poses challenges, however, due to h...

How to call SNV in RNA seq from Nanopore / Pacbio ? Easy: Clair-3RNA biorxiv.org/content/10.1... ~95% / ~96% F1-score for ONT / PacBio + we detect RNA editing! Great collaboration with Ruibang Luo, his group + Miten Jain ( need to invite them over here).
Special thanks to Justin Zook from GIAB!

The new chemistry requires less sample input, and Kinnex certainly reduces the isoSeq costs.

Successful classification of clinical pediatric leukemia genetic subtypes via structural variant detection using HiFi long-read sequencing Gene fusions are common primary drivers of pediatric leukemias and are the result of underlying structural variant (SVs). Current clinical workflows to detect such alterations rely on a multimodal app...

Confirmed utility of long reads in detecting fusion rearrangements in both HiFi WGS and IsoSeq.

www.medrxiv.org/content/10.1...