Jon Belyeu
@jonbelyeu.bsky.social
Bioinformatics scientist at PacBio, previously Illumina. I develop software tools in Rust and Python for genome analysis. https://orcid.org/0000-0001-5470-8299
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
GitHub - PacificBiosciences/Paraviewer
Contribute to PacificBiosciences/Paraviewer development by creating an account on GitHub.
github.com
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
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.
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.
link.springer.com
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
GitHub - PacificBiosciences/aardvark: A tool for sniffing out the differences in vari-Ants
A tool for sniffing out the differences in vari-Ants - PacificBiosciences/aardvark
github.com
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 10mo agoAardvark: Sifting through differences in a mound of variants https://www.biorxiv.org/content/10.1101/2025.10.03.680257v1
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:
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...
biorxiv.org
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...
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
doi.org
Interesting comparison between long-read sequencing techs for metagenomics: papers.ssrn.com/sol3/papers....
Culture-Independent Meta-Pangenomics Enabled by Long-Read Metagenomics Reveals Novel Associations with Pediatric Undernutrition
The human gut microbiome is associated with various forms of acute malnutrition, but current microbiome approaches are limited in resolution, often focused on c
papers.ssrn.com
“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...
GitHub - PacificBiosciences/pb-StarPhase: A phase-aware pharmacogenomic diplotyper for PacBio datasets
A phase-aware pharmacogenomic diplotyper for PacBio datasets - PacificBiosciences/pb-StarPhase
github.com
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😅:
Gang Fang@gangfang.bsky.social · 2y ago(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n
#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!
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...
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...
pacb.com