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Reposted by Dr. Sarah Carey

Ellie Armstrong @elliecat.bsky.social · 29/09/2026

If you saw me talk at PEQG or PAG and want to try out a new method for assembling sex chromosomes, our paper and pipeline are live! Biggest shoutout to @scarey.bsky.social for pioneering this method and happy to have played a part in its application and deployment!

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Dr. Sarah Carey @scarey.bsky.social · 29/09/2026

Lauren and Laramie are the best of the best and I'm privileged to have worked with them on this many-years endeavor. Thanks also to our collaborators @pbentz.bsky.social entz.bsky.social @elliecat.bsky.social & Alex Harkess for your insights on the analyses and pipeline! #SequenceAllDioeciousThings!

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Dr. Sarah Carey @scarey.bsky.social · 29/09/2026

3. CBS-Frontier (developed by @laramiemckenna.bsky.social): Interactive visualization of k-mers mapping to assembly The tools are available here: CBS-tools github.com/HudsonAlpha/... CBS-Frontier github.com/HudsonAlpha/...

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Dr. Sarah Carey @scarey.bsky.social · 29/09/2026

This work was led by the fabulous computational scientist Lauren Whitt, and there are three general steps in the pipeline: 1. CBS-Discovery: Create sex-specific k-mers lists from WGS of multiple isolates 2. CBS-Phase: Helper tools for quickly mapping CBS-Discovery k-mer lists to genome assembly

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Dr. Sarah Carey @scarey.bsky.social · 29/09/2026

I am thrilled to share our pre-print for CBS-tools: a k-mer based analysis that utilizes whole-genome sequencing of a few sex-identified isolates to guide users from the discovery of the heterogametic sex through identifying the sex-determination region www.biorxiv.org/content/10.6...

biorxiv.org

Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools

A complete reference genome for species with chromosomally-determined separate sexes should contain scaffolds for all sex chromosome homologs. However, sex chromosomes present distinct computational c...

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Reposted by Dr. Sarah Carey

Jacob Brandenburg @jbrandenburg13.bsky.social · 12/06/2025

This Father’s Day, we’re celebrating HiFi dad-a with some cutting-edge science! Researchers @elliecat.bsky.social at UC Riverside and @scarey.bsky.social at HudsonAlpha Institute for Biotechnology are revealing parts of the Y chromosome that were previously a mystery. www.pacb.com/blog/celebra...

pacb.com

Celebrating Father’s Day with new discoveries of the Y chromosome achieved with HiFi sequencing - PacBio

Featuring the Y chromosome - showcasing the power of HiFi sequencing to illuminate regions of the genome long considered out of reach

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Reposted by Dr. Sarah Carey

Ellie Armstrong @elliecat.bsky.social · 12/06/2025

@scarey.bsky.social and i wrote a fun piece about new possibilities with resolved Y chromosomes across the tree of life!

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Reposted by Dr. Sarah Carey

Laramie (Smith) Aközbek @laramiemckenna.bsky.social · 13/12/2024

It was such a joy to work on this project. Check out our lab’s recent project paper on the sex chromosomes of Amborella trichopoda in Nature Plants!

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Dr. Sarah Carey @scarey.bsky.social · 18/12/2024

Thank you! We used DEEPSPACE (github.com/jtlovell/DEE...), which builds off of GENESPACE. I don't think DEEPSPACE has a tutorial up for this just yet, but there's a vignette on the GENESPACE GitHub that walks through some of these steps htmlpreview.github.io?https://gith...

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Dr. Sarah Carey @scarey.bsky.social · 12/12/2024

Hi Bluesky! I'm going to use my first posts to tell you about some really exciting updates. I'm delighted to share that our manuscript on the Amborella sex chromosomes was published last month! www.nature.com/articles/s41...

nature.com

ZW sex chromosome structure in Amborella trichopoda - Nature Plants

The haplotype-resolved genome in Amborella trichopoda addresses outstanding questions on the structure and gene content of the recently evolved ZW sex chromosomes.

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