Matt Holt
@holtjma.bsky.social
Staff scientist at @PacBio; formerly @hudsonalpha; avid gamer; opinions are my own
We have released StarPhase v2.0! The key addition is support for PGx sub-allele definitions for genes from PharmVar. While we were in there, we made some other QoL upgrades as part of v2. Let us know what you think!
Full release notes: github.com/PacificBiosc...
Full release notes: github.com/PacificBiosc...
Release StarPhase v2.0.0 · PacificBiosciences/pb-StarPhase
Changes
Database construction (pbstarphase build) has been updated to support sub-allele definitions from PharmVar
Variants and alleles are now annotated as either being "core" or "sub" types
By ...
github.com
November 19, 2025 at 6:05 PM
We have released StarPhase v2.0! The key addition is support for PGx sub-allele definitions for genes from PharmVar. While we were in there, we made some other QoL upgrades as part of v2. Let us know what you think!
Full release notes: github.com/PacificBiosc...
Full release notes: github.com/PacificBiosc...
Reposted by Matt Holt
Long-read genome sequencing is new first-tier generic test in diagnostics of rare diseases
So satisfying to see a long journey end in best-possible diagnostic test for patients with rare diseases @radboudumc.bsky.social.
www.radboudumc.nl/en/news-item...
(1/n)
So satisfying to see a long journey end in best-possible diagnostic test for patients with rare diseases @radboudumc.bsky.social.
www.radboudumc.nl/en/news-item...
(1/n)
World first: Radboudumc pioneers new genetic test in clinical practice - New test is faster, more efficient, and provides more diagnoses for rare diseases
17 November 2025
www.radboudumc.nl
November 17, 2025 at 8:29 AM
Long-read genome sequencing is new first-tier generic test in diagnostics of rare diseases
So satisfying to see a long journey end in best-possible diagnostic test for patients with rare diseases @radboudumc.bsky.social.
www.radboudumc.nl/en/news-item...
(1/n)
So satisfying to see a long journey end in best-possible diagnostic test for patients with rare diseases @radboudumc.bsky.social.
www.radboudumc.nl/en/news-item...
(1/n)
Reposted by Matt Holt
Over Lansing, MI!
November 13, 2025 at 4:23 AM
Over Lansing, MI!
Reposted by Matt Holt
What we know, final edition of the night:
[Now in 3 parts]
—Prop 50 wins
—VA Dems flip Gov, LG, AG
—Dems gain leg seats in VA, NJ, & MS
—Dems defend NJ-Gov
—Dems win NJ+VA trifectas
—Mamdani wins
—PA Dems win state supreme court
—ME anti-mail voting measure loses
—GA Dems flip 2 statewide offices
[Now in 3 parts]
—Prop 50 wins
—VA Dems flip Gov, LG, AG
—Dems gain leg seats in VA, NJ, & MS
—Dems defend NJ-Gov
—Dems win NJ+VA trifectas
—Mamdani wins
—PA Dems win state supreme court
—ME anti-mail voting measure loses
—GA Dems flip 2 statewide offices
November 5, 2025 at 6:48 AM
What we know, final edition of the night:
[Now in 3 parts]
—Prop 50 wins
—VA Dems flip Gov, LG, AG
—Dems gain leg seats in VA, NJ, & MS
—Dems defend NJ-Gov
—Dems win NJ+VA trifectas
—Mamdani wins
—PA Dems win state supreme court
—ME anti-mail voting measure loses
—GA Dems flip 2 statewide offices
[Now in 3 parts]
—Prop 50 wins
—VA Dems flip Gov, LG, AG
—Dems gain leg seats in VA, NJ, & MS
—Dems defend NJ-Gov
—Dems win NJ+VA trifectas
—Mamdani wins
—PA Dems win state supreme court
—ME anti-mail voting measure loses
—GA Dems flip 2 statewide offices
Looking at code from 12+ months ago always feels like the uncanny valley of code self-review. There's evidence of my coding fingerprint, and I *know* I wrote the code, but it's not quite how I would do it today.
October 30, 2025 at 7:16 PM
Looking at code from 12+ months ago always feels like the uncanny valley of code self-review. There's evidence of my coding fingerprint, and I *know* I wrote the code, but it's not quite how I would do it today.
Reposted by Matt Holt
About half the GigaScience editorial board (incl me) just resigned (academic.oup.com/gigascience/... is not yet updated). I resigned because it is very unclear what is happening and why - see @scedmunds.bsky.social blog post gigasciencejournal.com/blog/and-its..., for eg
Editorial_Board
Editorial Team
Editor-in-Chief
Xun Xu, PhD; BGI Research, Shenzhen, China
Executive Editor
Hongling Zhou; GigaScience Press, BGI Shenzhen, China
Edito
academic.oup.com
October 29, 2025 at 4:03 PM
About half the GigaScience editorial board (incl me) just resigned (academic.oup.com/gigascience/... is not yet updated). I resigned because it is very unclear what is happening and why - see @scedmunds.bsky.social blog post gigasciencejournal.com/blog/and-its..., for eg
Reposted by Matt Holt
Hurricane Melissa is the THIRD Category 5 storm of 2025, tying the record set by the legendary 2005 season.
And get this, 80% of this season's hurricanes have reached Category 4 or 5 strength. That's the highest percentage in Atlantic history.
And get this, 80% of this season's hurricanes have reached Category 4 or 5 strength. That's the highest percentage in Atlantic history.
October 27, 2025 at 1:18 PM
Hurricane Melissa is the THIRD Category 5 storm of 2025, tying the record set by the legendary 2005 season.
And get this, 80% of this season's hurricanes have reached Category 4 or 5 strength. That's the highest percentage in Atlantic history.
And get this, 80% of this season's hurricanes have reached Category 4 or 5 strength. That's the highest percentage in Atlantic history.
Reposted by Matt Holt
Want a rare look inside @pacbio.bsky.social facility and hear how customers use HiFi for HLA typing and PGx? We made a 6-min documentary this summer. Check it out! www.youtube.com/watch?si=nXb...
Advancing human health with HiFi long-read sequencing
YouTube video by PacBio
www.youtube.com
October 23, 2025 at 4:15 PM
Want a rare look inside @pacbio.bsky.social facility and hear how customers use HiFi for HLA typing and PGx? We made a 6-min documentary this summer. Check it out! www.youtube.com/watch?si=nXb...
Our first major update for Aardvark since the pre-print is now available. We added an optional "record basepair" score type which may better match historical tandem repeat metrics, and also made some of the less-used metrics optional as well.
Full release notes here: github.com/PacificBiosc...
Full release notes here: github.com/PacificBiosc...
Release Aardvark v0.9.0 · PacificBiosciences/aardvark
Changes
Adds the optional RECORD_BP comparison type to all summary files. Review our methods for details on this metric. This metric is enabled with --enable-record-basepair-metrics.
The GT and BA...
github.com
October 20, 2025 at 7:52 PM
Our first major update for Aardvark since the pre-print is now available. We added an optional "record basepair" score type which may better match historical tandem repeat metrics, and also made some of the less-used metrics optional as well.
Full release notes here: github.com/PacificBiosc...
Full release notes here: github.com/PacificBiosc...
I think I just found my first AI generated preprint on bioRxiv. Unclear methodology, invalid citations, and dead links. Are these supposed to get reported somewhere?
October 20, 2025 at 2:36 PM
I think I just found my first AI generated preprint on bioRxiv. Unclear methodology, invalid citations, and dead links. Are these supposed to get reported somewhere?
Reposted by Matt Holt
Good evening. We estimate that between 4.2 and 7.6 million people turned out for the No Kings Day demonstrations held around the country on Saturday. This makes Oct 18 very likely the biggest single-day U.S. protest event since 1970. www.gelliottmorris.com/p/second-no-...
Second "No Kings Day" protests likely the largest single-day political demonstration since 1970, with 4.2-7.6 million participants
Here are the initial results from our crowdsourced crowd-counting estimates
www.gelliottmorris.com
October 19, 2025 at 3:17 AM
Good evening. We estimate that between 4.2 and 7.6 million people turned out for the No Kings Day demonstrations held around the country on Saturday. This makes Oct 18 very likely the biggest single-day U.S. protest event since 1970. www.gelliottmorris.com/p/second-no-...
Reposted by Matt Holt
Our third #ASHG25 CoLab begins in one hour at 10:15 am in Theater 1!
Hear from #PacBio and @epicypher.bsky.social on Fiber-seq epigenomics for integrated chromatin, genome, and methylome insights, plus Revio workflow updates and big announcements on what’s next for #Revio and #Vega in 2026 👀.
Hear from #PacBio and @epicypher.bsky.social on Fiber-seq epigenomics for integrated chromatin, genome, and methylome insights, plus Revio workflow updates and big announcements on what’s next for #Revio and #Vega in 2026 👀.
October 17, 2025 at 1:15 PM
Our third #ASHG25 CoLab begins in one hour at 10:15 am in Theater 1!
Hear from #PacBio and @epicypher.bsky.social on Fiber-seq epigenomics for integrated chromatin, genome, and methylome insights, plus Revio workflow updates and big announcements on what’s next for #Revio and #Vega in 2026 👀.
Hear from #PacBio and @epicypher.bsky.social on Fiber-seq epigenomics for integrated chromatin, genome, and methylome insights, plus Revio workflow updates and big announcements on what’s next for #Revio and #Vega in 2026 👀.
I’ll be presenting a poster on Mitorsaw for #PacBio HiFi mitochondrial analysis today! Come see me this afternoon at #ASHG25 poster #4050 to chat about that or other topics!
I'm heading to Boston for #ASHG25 tomorrow, let me know if you'd like to chat about using HiFi sequencing for mitochondrial analyses, pharmacogenomics, or anything else!
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)
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
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
October 17, 2025 at 11:48 AM
Reposted by Matt Holt
Eric Green receiving the ASHG Leadership Award. Talks about being the first institute or center director to lose his leadership role. Said that he failed to doge the bullet. #ASHG25
October 16, 2025 at 8:49 PM
Eric Green receiving the ASHG Leadership Award. Talks about being the first institute or center director to lose his leadership role. Said that he failed to doge the bullet. #ASHG25
Reposted by Matt Holt
ASHG Plenary Session starting with the awards ceremony honoring Eric Green with the Leadership Award of @geneticssociety.bsky.social reflecting on his career in human genetics & genomics leading the Human Genome Project & the NHGRI and the leadership principles he has learned throughout #ASHG25
October 16, 2025 at 8:47 PM
ASHG Plenary Session starting with the awards ceremony honoring Eric Green with the Leadership Award of @geneticssociety.bsky.social reflecting on his career in human genetics & genomics leading the Human Genome Project & the NHGRI and the leadership principles he has learned throughout #ASHG25
Reposted by Matt Holt
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...
WGS data: pacificbiosciences.github.io/ParaviewerWG...
PureTarget data: pacificbiosciences.github.io/ParaviewerPT...
Paraviewer
pacificbiosciences.github.io
October 15, 2025 at 2:59 PM
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...
WGS data: pacificbiosciences.github.io/ParaviewerWG...
PureTarget data: pacificbiosciences.github.io/ParaviewerPT...
Reposted by Matt Holt
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
October 15, 2025 at 2:58 PM
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
Reposted by Matt Holt
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
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
October 15, 2025 at 2:24 PM
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
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
Reposted by Matt Holt
#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
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
October 14, 2025 at 3:33 PM
#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
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
Reposted by Matt Holt
📣 PacBio Announces Major Advances for #Revio and #Vega to Lower Genome Cost and Expand Multiomic Capabilities
New SPRQ-Nx chemistry: HiFi genome for less than $300 🧪 🧬
#HiFi #LongReads #SPRQ_Nx #BetaAccess #SMRTcell #ReusableChip @pacbio.bsky.social
investor.pacificbiosciences.com/news-release...
New SPRQ-Nx chemistry: HiFi genome for less than $300 🧪 🧬
#HiFi #LongReads #SPRQ_Nx #BetaAccess #SMRTcell #ReusableChip @pacbio.bsky.social
investor.pacificbiosciences.com/news-release...
October 14, 2025 at 2:21 PM
📣 PacBio Announces Major Advances for #Revio and #Vega to Lower Genome Cost and Expand Multiomic Capabilities
New SPRQ-Nx chemistry: HiFi genome for less than $300 🧪 🧬
#HiFi #LongReads #SPRQ_Nx #BetaAccess #SMRTcell #ReusableChip @pacbio.bsky.social
investor.pacificbiosciences.com/news-release...
New SPRQ-Nx chemistry: HiFi genome for less than $300 🧪 🧬
#HiFi #LongReads #SPRQ_Nx #BetaAccess #SMRTcell #ReusableChip @pacbio.bsky.social
investor.pacificbiosciences.com/news-release...
We just released a major update for StarPhase that adds support for inexact matching PGx alleles. We're hoping this streamlines the process for discovering novel allele combinations with #PacBio #HiFi data, feedback welcome!
Full notes here: github.com/PacificBiosc...
#ASHG25
Full notes here: github.com/PacificBiosc...
#ASHG25
Release StarPhase v1.5.0 · PacificBiosciences/pb-StarPhase
Changes
Adds a new field to the output json, inexact_diplotypes. This field is intended to capture information about inexact allele matches. The behavior of this output depends on the gene:
For s...
github.com
October 13, 2025 at 8:13 PM
We just released a major update for StarPhase that adds support for inexact matching PGx alleles. We're hoping this streamlines the process for discovering novel allele combinations with #PacBio #HiFi data, feedback welcome!
Full notes here: github.com/PacificBiosc...
#ASHG25
Full notes here: github.com/PacificBiosc...
#ASHG25
I'm heading to Boston for #ASHG25 tomorrow, let me know if you'd like to chat about using HiFi sequencing for mitochondrial analyses, pharmacogenomics, or anything else!
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)
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
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
October 13, 2025 at 1:48 PM
I'm heading to Boston for #ASHG25 tomorrow, let me know if you'd like to chat about using HiFi sequencing for mitochondrial analyses, pharmacogenomics, or anything else!
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)