Billy
@williamrowell.dev
Geneticist, ersatz programmer, data nerd, comedy lover, and recovering academic. Trying to make it easier for people to analyze and interpret biological data. Bioinformatics Scientist @PacBio.bsky.social
Reposted by 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
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
April 24, 2025 at 3:34 PM
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
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
Reposted by Billy
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...
www.nature.com/articles/s41...
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...
www.nature.com
April 23, 2025 at 4:11 PM
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...
www.nature.com/articles/s41...
Reposted by Billy
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...
www.biorxiv.org
April 22, 2025 at 2:21 PM
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:
Reposted by Billy
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 ✊
April 12, 2025 at 12:22 AM
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 ✊
Reposted by Billy
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.
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...
2025.eshg.org
April 10, 2025 at 3:41 PM
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.
Reposted by Billy
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...
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
April 10, 2025 at 3:41 PM
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...
doi.org/10.1093/bioi...
Reposted by Billy
Get in Dorks, we are going protesting.
STAND UP FOR SCIENCE. MARCH 7th 12-4pm. DC AND YOUR STATE CAPITALS.
More information to come.
STAND UP FOR SCIENCE. MARCH 7th 12-4pm. DC AND YOUR STATE CAPITALS.
More information to come.
February 9, 2025 at 2:23 PM
Get in Dorks, we are going protesting.
STAND UP FOR SCIENCE. MARCH 7th 12-4pm. DC AND YOUR STATE CAPITALS.
More information to come.
STAND UP FOR SCIENCE. MARCH 7th 12-4pm. DC AND YOUR STATE CAPITALS.
More information to come.
Reposted by Billy
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
February 11, 2025 at 4:40 AM
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
Reposted by Billy
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...
www.sciencedirect.com/science/arti...
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…
www.sciencedirect.com
January 13, 2025 at 4:31 PM
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...
www.sciencedirect.com/science/arti...
Reposted by Billy
“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...
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
December 11, 2024 at 2:30 PM
“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...
Pre-print: doi.org/10.1101/2024...
Repo: github.com/PacificBiosc...
Reposted by Billy
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
November 23, 2024 at 2:59 PM
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
Reposted by Billy
@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
November 23, 2024 at 7:23 PM
@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
Reposted by Billy
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
Please spread the word
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...
pacb.com
November 19, 2024 at 9:46 PM
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
Please spread the word
Reposted by Billy
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
November 19, 2024 at 9:46 PM
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
Reposted by Billy
Waking up in my own normal body and freaking out like the guy who woke up as a bug
February 9, 2024 at 2:58 PM
Waking up in my own normal body and freaking out like the guy who woke up as a bug
Reposted by Billy
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...
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...
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...
www.biorxiv.org
October 30, 2024 at 3:31 PM
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...
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...
Reposted by Billy
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...
- Input requirements drop from 2 micrograms to 500 nanograms (per SMRT cell)
- 30% increase yield per cell (~90Gb -> 120Gb)
www.pacb.com/press_releas...
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...
www.pacb.com
October 29, 2024 at 2:06 PM
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...
- Input requirements drop from 2 micrograms to 500 nanograms (per SMRT cell)
- 30% increase yield per cell (~90Gb -> 120Gb)
www.pacb.com/press_releas...
Reposted by Billy
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.
March 15, 2024 at 5:45 PM
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.
Reposted by Billy
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.
March 15, 2024 at 6:03 PM
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.
Reposted by Billy
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...
Release here: github.com/PacificBiosc...
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 ....
github.com
February 9, 2024 at 6:39 PM
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...
Release here: github.com/PacificBiosc...
Reposted by Billy
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...
“HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing”: doi.org/10.1093/bioi...
January 26, 2024 at 3:07 PM
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...
“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.
January 13, 2024 at 7:53 AM
Listening to _Four Thousand Weeks_ at 2x speed to save time.