Jon Belyeu

Paraviewer creates easy-to-use review websites from Paraphase output. Try these demos!

WGS data: pacificbiosciences.github.io/ParaviewerWG...

PureTarget data: pacificbiosciences.github.io/ParaviewerPT...

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

Attending #ASHG25? Visit #PacBio at booth 919!

Connect with our team, explore live demos of #Vega, and discover the latest in long-read sequencing. While you’re there, enter our daily Labubu drawing!

See the full program here: bit.ly/4nmBnfn

#ASHG #HumanGenomics #ASHG2025

GitHub - PacificBiosciences/SVTopo: Complex structural variant visualization for HiFi sequencing data Complex structural variant visualization for HiFi sequencing data - PacificBiosciences/SVTopo

Tool (with demos) available at github.com/PacificBiosc...

Here's an example from the paper: a complex rearrangement shown with svtopo (top), IGV (middle), and Ribbon (bottom):

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.

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

Install SVTopo from conda, or go straight to the source at github.com/PacificBiosc.... If you break it, let me know! The best way is by creating a github issue on the repo.

In addition to making these handy-dandy images, SVTopo creates a serverless table browser to sort, filter, and view the results. The one for these 7 samples is live at pacificbiosciences.github.io/SVTopo/. Try it out!

This example might look at first glance like a bad representation of a translocation, but the SVA annotation is a giveaway - reads from chr12 and chr19 aligned to a random SVA retrotransposon rather than a real connection between three chromosomes.

Alignment challenges mean that the visualization doesn’t always work, of course. 125 images from these 7 genomes had alignment artifacts that made them useless for variant interpretation. Many of these appear to be useful in another way, though – identification of false positives.

We looked at SVTopo images for 7 unrelated samples (HG002 and 6 from the platinum pedigrees cohort: 10.1101/2024.10.02.616333) and observed 142 unique complex SVs that we put in 11 categories (fig2).

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)

Although there are some excellent genome visualization tools out there, none of them are great at representing the complex structural variation that long reads uniquely identify. SVTopo is for this. Shows alignments in new genomic blocks and represents those blocks relative to the reference genome.

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:

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...

Interesting comparison between long-read sequencing techs for metagenomics: papers.ssrn.com/sol3/papers....

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...

Another very insightful paper on #methylation and long-read sequencing by @gangfang.bsky.social, describing some important but frequently overlooked caveats.

Gang provides a fantastic summary in his post, but here's my take too😅:

If you were interested but missed it: www.pacb.com/wp-content/u...

#ASHG2024 was a blast. I had great discussions with friends and #pacbio collaborators, presented a poster on my new tool SVTopo, welcomed #PacBioVega to the world, and realized than I'm a bigger fan of One Republic than I knew before. Excited for next time!

PacBio Unveils the Vega System, a New Sequencing Platform Bringing HiFi to the Benchtop - PacBio Priced at just $169,000 Vega is designed to make highly accurate long-read sequencing accessible to any laboratory Translations:  Japanese  |  Chinese  |  Korean MENLO PARK, Calif., Nov. 06, 2024 (GLO...

It's official, #PacBio has launched a new benchtop sequencer!

Quick summary of the new Vega system:
- instrument = $169k
- consumables = $1100 per run
- output = 60 Gbp, 24 hr run time

This is the #HiFi sequencer #microbiology labs have been asking for.

www.pacb.com/press_releas...

Glad to see the interest! Associating individual alignments with VCF breakend coordinates can be challenging, which is why the recommended workflow uses sawfish (we added a sawfish read output to make it work) but svtopo can also run with just the HiFi bam for samples without sawfish calls