🐧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
mastodon 4.7.3(he/him) Genomics Researcher. The Kākāpō Genomics Guy. Theoretical Genomicist. Annotation Artist. #Conservation #Bioinformatics #Rust #CompBio 🦀 #genomics #fedi22 #CompBio #popgen #Annotation #Stats #MachineLearning 🏳️🌈
611 Followers
570 Following
18 Posts
Joined November 05, 2022
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Guide: Switching from Conda/Mamba to Pixi. Near instant environments, better HPC compatibility and reproducibility. But really, it's the speed!
Saving Kākāpō with Genomics - Check out this video!
"What if... genomics could help save an endangered species?"
#kakapo #conservation #genomics #aotearoa #newzealand #bird #animals
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
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/
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
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
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!
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 💍
#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
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
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
Minimap2 library for Python: https://pypi.org/project/minimappers2/
Very much alpha stage, but multithreading is supported. Results are returned in DataFrames.
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
New update to the #minimap2 #rust crate. Experimental multithread support.
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!