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Matt Holt

@holtjma.bsky.social

870 followers 150 following 200 posts

Staff scientist at @PacBio; formerly @hudsonalpha; avid gamer; opinions are my own

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Reposted by Matt Holt

PacBio @pacbio.bsky.social · 2h

Just in: #PacBio HiFi long-read sequencing is powering the National Institute on Aging’s Long Life Family Study.

Up to 7,800 genomes and epigenomes will be sequenced on Revio systems to uncover rare variants, methylation patterns, and other factors linked to healthy aging.

🔗 bit.ly/3IUDdFo

Reposted by Matt Holt

Rob Patro @robp.bsky.social · 1h

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

Postdoc Description.docx

Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

docs.google.com

Reposted by Matt Holt

Jacob Schreiber @jmschreiber91.bsky.social · 1d

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!

The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

Reposted by Matt Holt

Rob Patro @robp.bsky.social · 1d

It absolutely warms my heart when I click on a pre-print that includes a bunch of top methods folks from industry and I see (1) open-source software (with a good license; MIT in this case) that is (2) written in Rust. Bravo @pacbio.bsky.social!

Moar Rust plz!

github.com/PacificBiosc...

Matt Holt @holtjma.bsky.social · 1d

We're quite happy with how this first version of Aardvark turned out, and we are actively working on additions! If you have any suggestions, please let us know here or on GitHub!

Special thanks to all our collaborators and beta users for the initial wave of feedback!

(8/8)

Matt Holt @holtjma.bsky.social · 1d

So in summary, Aardvark:

1. Adds a new sequence-centric "basepair" scoring scheme
2. Enables comparisons of new types of variants (TRs & SVs)
3. Includes a traditional genotype score
4. Calculates everything really fast!
5. Almost forgot, it's fully open-source!

(7/N)

Matt Holt @holtjma.bsky.social · 1d

Even if you do not (yet) fully buy in to basepair scoring, Aardvark includes a traditional genotype score... and it calculates both sets of scoring metrics *really* fast!

For small variants, on average 16x faster than hap.py, with most runs finishing <2 minutes (16 threads).

(6/N)

Matt Holt @holtjma.bsky.social · 1d

Since Aardvark looks at sequences, it enables some comparisons that were previously very challenging:

1. Tandem repeat (TR) v. TR benchmarking
2. TR v. small variant benchmarking
3. Structural variant (SV) benchmarking
4. Joint benchmarking (small + SV)

(5/N)

Matt Holt @holtjma.bsky.social · 1d

With basepair scoring, we instead:

1. Mask all variants, only *sequences* are compared. Equivalent representations will receive identical scores!
2. Score each modified basepair independently, enabling implicit partial credit while removing biases from representation

(4/N)

Matt Holt @holtjma.bsky.social · 1d

There were two driving forces behind the basepair score:

1. Equivalent variant representations can be scored inconsistently with a genotype approach
2. Traditional genotype scoring has no concept of partial credit, it's either 100% correct or 100% wrong

(3/N)

Matt Holt @holtjma.bsky.social · 1d

The main addition in Aardvark is the "basepair" scoring scheme, which compares local haplotype *sequences* instead of variants and genotypes. See the attached figure for a quick example of how basepair scoring compares to genotype scoring.
(2/N)

Matt Holt @holtjma.bsky.social · 1d

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

Matt Holt @holtjma.bsky.social · 3d

Feels like they should be called chromalots at that point #dadjokes

Bryan White, MS Bio, MPH 🧬 @crvscience.com · 3d

Homie got 229 pairs of chromosomes

www.sciencedaily.com/releases/202...

This tiny butterfly has the most chromosomes of any animal on Earth

Scientists have confirmed that the Atlas blue butterfly carries the most chromosomes of any animal, with 229 pairs. Unlike duplication, its chromosomes split apart, reshaping its genome in surprising ...

www.sciencedaily.com

Matt Holt @holtjma.bsky.social · 9d

😢

Matt Holt @holtjma.bsky.social · 9d

Before and/or after losing Lamar?

Reposted by Matt Holt

PacBio @pacbio.bsky.social · 11d

🎉 #PacBio is turning 25 and we are bringing the #PacBioBlockParty to #ASHG25. Join us for a night of celebration with the genomics community.

And a big thanks to our sponsors for their support: SPT Labtech, Twist Bioscience, Hamilton, and n6!

Spaces are filling up fast! RSVP today: bit.ly/46xnUeI

Reposted by Matt Holt

Javier Santoyo @jsantoyo.bsky.social · 12d

Advances in haplotype phasing and genotype imputation. #HaplotypePhasing #GenomeImputation @natrevgenet.nature.com
www.nature.com/articles/s41...

Reposted by Matt Holt

Elinne Becket, PhD @bielleogy.bsky.social · 15d

Giving a webinar on #BlueSoup this Friday, in case anyone wants to pop in during their lunch!

A promotional flyer for a webinar in the CSU Bioinformatics Webinar Series. On the left side, it shows the date and time: “26 Sep | 12 PM PST.” It includes instructions to join via Zoom with Meeting ID: 886 2442 3158 and a QR code above. On the right, there is a photo of Dr. Elinne Becket, Associate Professor in the Department of Biological Sciences at California State University San Marcos, sitting outdoors with plants and trees in the background. Below, the title of the talk is displayed: “The Soup that Blue up Twitter.” The description explains that Dr. Becket will discuss the shared curiosity of science, open science, and a story from February 2023 when leftover beef soup prepared by her mom turned bright blue. Scientists and people on Twitter collaborated to investigate, leading to a global effort among microbiologists and chemists. At the bottom, there are links to learn more about upcoming webinars at www.informatics.sdsu.edu and Dr. Becket’s website: https://elinneb.wixsite.com/becketlab

Reposted by Matt Holt

Adam Phillippy @aphillippy.bsky.social · 16d

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

www.biorxiv.org

Reposted by Matt Holt

Kat Abughazaleh @katmabu.bsky.social · 18d

That’s me in the video. And a Fox News host just celebrated me being assaulted by ICE.

If ICE will do this to a congressional candidate with a big platform, just imagine what they’re doing to the people they’re kidnapping.

Acyn @acyn.bsky.social · 18d

Ingraham: A Democrat congressional candidate was thrown to the ground by an ICE agent. Good work

Matt Holt @holtjma.bsky.social · 18d

Only if they’re calling each other

Matt Holt @holtjma.bsky.social · 20d

If nothing else, the k-mer representation here definitely looks promising! Thanks for sharing this!

Matt Holt @holtjma.bsky.social · 21d

That was basically the backup plan if I couldn’t find something fully baked already. Mostly to avoid reinventing the wheel and the hope that all the subtleties would already be handled.

Matt Holt @holtjma.bsky.social · 21d

When you get no recommendations on your “Does X exist?” post…

Matt Holt @holtjma.bsky.social · 21d

Question for the rust-bio folks: any recommendations on a dynamic de-bruijn graph crate?

I found some DBG crates but they seem to be A) unmaintained and/or B) not for dynamic applications.