@josephguhlin@sci.kiwi

Joseph Guhlin @josephguhlin@sci.kiwi · Oct 28, 2025

🐧We researched one of the world’s rarest #penguins. The yellow‑eyed penguin (aka hoiho/takaraka) isn’t one homogeneous species after all!

www.biorxiv.org/content/10.1...

#hoiho #conservation #genomics #birds #nzwildlife #endangered #wildlife #nature

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Joseph Guhlin @josephguhlin@sci.kiwi · Jan 08, 2025

Guide: Switching from Conda/Mamba to Pixi. Near instant environments, better HPC compatibility and reproducibility. But really, it's the speed!

https://josephguhlin.com/pixi-uv-bioinformatics-powerhouse/

#bioinformatics #genomics #python

josephguhlin.com

Pixi/uv: Bioinformatics Powerhouse – Joseph Guhlin: Bioinformatics and Genomics

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Joseph Guhlin @josephguhlin@sci.kiwi · Aug 29, 2024

Saving Kākāpō with Genomics - Check out this video!

"What if... genomics could help save an endangered species?"

#kakapo #conservation #genomics #aotearoa #newzealand #bird #animals

https://www.rnz.co.nz/programmes/what-if-genomics-in-aotearoa/story/2018952806/what-if-genomics-could-help-save-an-endangered-species

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Joseph Guhlin @josephguhlin@sci.kiwi · Mar 21, 2024

ORF landscape of chr1 Nasonia vitripennis, ORFS >= 150 aa in length. ORFs are sized relative to each other. Locations spawned from are accurate.
It's a web app! https://orfs.sci.kiwi

Made for a presentation to show just how many ORFs there are in a single chromosome. It's fun to play around with the settings, though. You can upload your own chromosome, and it's processed in real time (it takes a few minutes to load!).

#rust #rustlang #bevy #genomics #bioinformatics

Made with @bevy@mastodon.social

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Joseph Guhlin @josephguhlin@sci.kiwi · Mar 16, 2024

minimap2-rs updated! Now using minimap 2.27. Needletail + rayon support! Thanks for all the pull requests to help get this here!

https://crates.io/crates/minimap2
All changes: https://github.com/jguhlin/minimap2-rs/?tab=readme-ov-file#0117-minimap2-227
#rust #bioinformatics #genomics #nanopore #pacbio #RustLang

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Joseph Guhlin @josephguhlin@sci.kiwi · Mar 11, 2024

A blog post! Improving the SFASTA index with B+ Trees then moving to Fractal trees, and some ideas. High-performance #bioinformatics from a pop geneticist. #rust
Definitely open to more ideas!

https://josephguhlin.com/sfasta-fast-index-building/

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Joseph Guhlin @josephguhlin@sci.kiwi · Sep 12, 2023

Unity's new pricing structure is another reason to build your stuff with Open Source engines. Yeah, you've got to have a bit more skill to get to the dream product, but you aren't restricted. #godot #bevy

sci.kiwi

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Joseph Guhlin @josephguhlin@sci.kiwi · Aug 28, 2023

Our paper made the news (and is finally out)!

https://www.nzherald.co.nz/waikato-news/news/saving-the-kakapo-the-smart-science-helping-pull-our-parrot-back-from-the-brink/3A7RGDM6OVCVNIFKQ5I6OQUBME/

#kakapo #nz #aotearoa #conservation #birds #genomics

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Joseph Guhlin @josephguhlin@sci.kiwi · Aug 23, 2023

Announcing minimap2-rs 0.1.15 release - Biggest features are compilation on aarch64, and better support for static builds. Also reduced dependency version to remove unnecessary tokio dependencies. Thanks again to the contributors helping me with this code!

Changelog: https://github.com/jguhlin/minimap2-rs#0115-minimap2-226

Crate: https://crates.io/crates/minimap2

Sys Crate: https://crates.io/crates/minimap2-sys

#rust #nanopore #pacbio #bioinformatics #genomics

GitHub

GitHub - jguhlin/minimap2-rs: Rust bindings to minimap2 library

Rust bindings to minimap2 library. Contribute to jguhlin/minimap2-rs development by creating an account on GitHub.

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Joseph Guhlin @josephguhlin@sci.kiwi · Aug 03, 2023

SEMINAR: Species-wide genomics of kākāpō provides transformational tools to accelerate recovery

Tēnā koutou katoa

A reminder about our Genomics Aotearoa seminar, online this Friday, August 4 at 3pm. (NZ Time)

Join from PC, Mac, iOS, or Android:
https://otago.zoom.us/j/97097442106?pwd=RlczU3VCdFBmbmt4Yng4VW5OcHdSdz09

It will also be recorded and on YouTube at a later date. :)

#conservation #bioinformatics #genomics #science #sciencemastodon #birds #avian

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Joseph Guhlin @josephguhlin@sci.kiwi · Jun 06, 2023

This is important; the datasets I've downloaded had the "raw" and "processed" data as identical. Although I believe those practices were better than most in this study (all reads were retrained, not just aligned ones!). #genomics #bioinformatics #adna

"Improving data archiving practices in ancient genomics"

https://www.biorxiv.org/content/10.1101/2023.05.15.540553v1.full

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Joseph Guhlin @josephguhlin@sci.kiwi · May 19, 2023

#Minimap2 #Rust library release: minimap2 v0.1.13+minimap2.2.26

* Latest minimap2 stable release (2.26)
* with_seq function
* hopefully compiles for MacOS / aarch64.
* Still struggling with SSE, I recommend using simde feature
* Soft-clipping properly in CIGAR strings but use caution. Happy to work on it more.

https://github.com/jguhlin/minimap2-rs

https://crates.io/crates/minimap2

And the -sys crate
https://crates.io/crates/minimap2-sys

#bioinformatics #genomics #nanopore #pacbio

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Joseph Guhlin @josephguhlin@sci.kiwi · Jan 20, 2023

Minimap2 library for Python: https://pypi.org/project/minimappers2/

Very much alpha stage, but multithreading is supported. Results are returned in DataFrames.

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Joseph Guhlin @josephguhlin@sci.kiwi · Jan 19, 2023

Minimap2 #Rust bindings v0.1.11 release. This release is built mainly thanks to others! New features:

* HTS Lib support to write out SAM/BAM files
* mm2-fast feature flag to replace minimap2 (no API changes)
* SIMD everywhere compilation feature flag now working
* More tests
* Proper Display impl for Strand
* Better optional quality scores in HTS lib

See: https://crates.io/crates/minimap2#features to enable.

https://crates.io/crates/minimap2

Docs.rs is compiling the new docs

#Bioinformatics #Genomics #Nanopore

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Joseph Guhlin @josephguhlin@sci.kiwi · Nov 22, 2022

This looks cool:

One tool to rule the types,
One tool to FFI them,
One tool to parse your Rust,
And in the darkness, compile them 💍

https://github.com/1Password/typeshare

#Rust

GitHub

GitHub - 1Password/typeshare: Typeshare is the ultimate tool for synchronizing your type definitions

Typeshare is the ultimate tool for synchronizing your type definitions between Rust and other languages for seamless FFI. - 1Password/typeshare

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Joseph Guhlin @josephguhlin@sci.kiwi · Nov 22, 2022

This paper has not gotten enough attention! We are moving towards large-scale genomics. They reannotated 488 genomes in a comparative way!
"TOGA integrates gene annotation with orthology inference at scale"

https://www.biorxiv.org/content/10.1101/2022.09.08.507143v1

We know phylogenomics can suffer from anno-metho bias: https://pubmed.ncbi.nlm.nih.gov/35588743/

#Bioinformatics #Genomics

bioRxiv

TOGA integrates gene annotation with orthology inference at scale

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, which limits scalability. We prese

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Joseph Guhlin @josephguhlin@sci.kiwi · Nov 15, 2022

New update to the #minimap2 #rust crate. Experimental multithread support.

https://crates.io/crates/minimap2

#bioinformatics #genomics

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Joseph Guhlin @josephguhlin@sci.kiwi · Nov 13, 2022

In 3 weeks, our #Conservation paper has 687 full-text reads! (Incl. ones on researchgate).

I think one of the strengths is using #ProbabilisticProgramming for small populations, letting us do #GWAS and #PopGen better and providing useful estimates back to the conservation practitioners. Lots of other strengths too (high-quality SNP calling) and correcting the record of analyses based off of incomplete genome annotation!

https://www.biorxiv.org/content/10.1101/2022.10.22.513130v1

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Joseph Guhlin

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Pixi/uv: Bioinformatics Powerhouse – Joseph Guhlin: Bioinformatics and Genomics

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GitHub - jguhlin/minimap2-rs: Rust bindings to minimap2 library

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GitHub - 1Password/typeshare: Typeshare is the ultimate tool for synchronizing your type definitions

TOGA integrates gene annotation with orthology inference at scale

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