Jon Belyeu (@jon_belyeu) header
Jon Belyeu (@jon_belyeu) profile picture

Jon Belyeu

@jon_belyeu

Bioinformatics scientist at PacBio. Views expressed are my own and not those of employer, etc.

 Salt Lake City, UT
jonbelyeu.com/
Joined September 2015
  • Tweets149
  • Following222
  • Followers307
18Media
Photo by Jon Belyeu (@jon_belyeu)Photo by Jon Belyeu (@jon_belyeu)Photo by Jon Belyeu (@jon_belyeu)Photo by Jon Belyeu (@jon_belyeu)Photo by Jon Belyeu (@jon_belyeu)Photo by Jon Belyeu (@jon_belyeu)Photo by Jon Belyeu (@jon_belyeu)Photo by Jon Belyeu (@jon_belyeu)Photo by Jon Belyeu (@jon_belyeu)
I just released a new preprint! The manuscript describes SVTopo, a software tool that enhances visualization of complex SVs using HiFi data: biorxiv.org/content/10.1101/…
Complex structural variant visualization with SVTopo

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 rearrangem...

biorxiv.org
1
4
118
I'm starting to transition away from here so I wrote a longer summary of the manuscript where the skies are blue 🦋. If you aren't on there yet, there's no time like the present 😀
53
Sometimes vaccine efficacy is subtle Sometimes it isn't
Image from Neil Stone (@DrNeilStone)
640
7,863
218
52,305
1,882,873
Jon Belyeu retweeted
Matt Holt (@holtjma) profile picture
Matt Holt@holtjma11 Dec 2024
“StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data” is now available online! In this work, we explore the use of long-read sequencing (#PacBio #HiFi) for #pharmacogenomics #PGx. 1/2
1
3
11
258
Jon Belyeu retweeted
Daniel Portik (@DPortik) profile picture
Daniel Portik@DPortik7 Nov 2024
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. pacb.com/press_releases/pacb…
PacBio Unveils the Vega System, a New Sequencing Platform Bringing HiFi to the Benchtop - PacBio

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...

pacb.com
4
36
4
111
14,808
I'm happy to announce that SVTopo, a new computational tool from PacBio (github.com/PacificBioscience…), is ready for you to try. SVTopo creates simple images so you can rapidly understand complex changes in genome structure. See me and learn more at ASHG 2024 in Denver, poster 1180W
GitHub - PacificBiosciences/SVTopo: Complex structural variant visualization for HiFi sequencing...

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

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

github.com
2
22
61
5,169
more replies
I wrote SVTopo to make it easier to understand structural variants like: inversions with flanking deletions/duplications; non-tandom inversions, non-tandem duplications; translocations; and combination rearrangements of deletion, duplication, inversion, etc. #PacBio #HiFi
1
1
214
Check out these examples (from HG002): github.com/PacificBioscience…
3
153
Happy to introduce sawfish, a new HiFi structural variant caller emphasizing local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis contexts: 1/n doi.org/10.1101/2024.08.19.6…
2
20
1
63
10,707
A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree biorxiv.org/cgi/content/shor… #biorxiv_genomic
24
1
36
5,102
I’m happy to say that we’ve just released a manuscript on bioRxiv describing our new tool TRGT-denovo. This new method was developed by Tom Mokveld and @egor_dolzhenko along with the help of many collaborators (1/n) biorxiv.org/content/10.1101/…
TRGT-denovo: accurate detection of de novo tandem repeat mutations

TRGT-denovo: accurate detection of de novo tandem repeat mutations

Motivation Identifying de novo tandem repeat (TR) mutations on a genome-wide scale is essential for understanding genetic variability and its implications in rare diseases. While PacBio HiFi sequen...

biorxiv.org
1
20
1
47
5,217
Jon Belyeu retweeted
Matt Holt (@holtjma) profile picture
Matt Holt@holtjma26 Jan 2024
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/bioinformati…
Matt Holt (@holtjma) profile pictureMatt Holt@holtjma30 Oct 2023
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: github.com/PacificBioscience…
Release HiPhase v1.0.0 · PacificBiosciences/HiPhase

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...

github.com
2
20
1
44
7,451
Characterization and visualization of tandem repeats at genome scale go.nature.com/3TKX7FF
Image from Nature Biotechnology (@NatureBiotech)
1
55
5
171
47,522
Great @biorxivpreprint: how you can call LPA CNV from @illumina WGS. This is a sig. step forward for studying #cardiovascular risk. 60% of samples report phased CNV -> improves phenotype correlation. @BCM_HGSC @MikeEberle @jon_belyeu @srbehera11 biorxiv.org/content/10.1101/…
Image from Fritz Sedlazeck (@sedlazeck)
1
12
28
4,300
Hello #ASHG22! Check out poster PB2257 to learn how we call copy number in the LPA region with #illumina WGS. I’ll be at the poster between 3-4:45 tomorrow
4
6
16
In case you’re interested but not present:
Image from Jon Belyeu (@jon_belyeu)
1
5
14
Checkout PB2257 #ASHG22 by #Illumina's @jon_belyeu, @sedlazeck and Baylor U. They show how to estimate total and allele-specific KIV-2 repeat length, which strongly impacts #CVD risk. A challenging genomic region that provides enormous medical insight, coming to #DRAGEN soon.
5
15
At #ASHG22 next week, we will have Illumina bioinformatics developers present three posters throughout the week. PB2257: LPA calling from WGS PB2906: Graph alignment for medically relevant genes PB2751: #PGx from #WGS
4
14
Very happy to share my first research article @illumina on genotyping HBA1 and HBA2 genes from whole-genome sequencing data: illumina.com/science/genomic….
Genotyping of high homology HBA1 and HBA2 from Illumina whole-genome sequencing

Genotyping of high homology HBA1 and HBA2 from Illumina whole-genome sequencing

illumina.com
4
9
1
35
Load more