Data Science Team Training: Building data science capacity in the public health workforce. I'm writing a (free) e-book for public health practitioners upskilling in data science, as part of my work with the CSTE's DSTT program. blog.stephenturner.us/p/data-scien...
@psy-fer.bsky.social , don't you have one?
Unfortunately, @nanoporetech.com really dropped the ball on the cost aspect by killing their P2 Solo line. Those devices were cheap, and had a low ongoing service / warranty cost, so were ideal for small to medium-scale research labs.
PacBio doesn't have anything to target that market either... 🤷♀️.
Not nearly as polished, but I'm currently writing my thesis and it overlaps many of these topics
My thesis also covers a bunch of this. Specifically the chapters introducing pairwise alignment and minimizers:
curiouscoding.nl/categories/t...
Looks very cool: fastVEP: A Fast, Comprehensive Variant Effect Predictor Written in Rust www.biorxiv.org/content/10.6...
What about Computeral Bioinfology?
Check it again, there are even more now
What about the computational biologist versus bioinformatician difference debate?
GALBA2 is walking into the arena. github.com/Gaius-August... Fully ported to snakemake, accuracy matches old galba.pl , similar features as BRAKER4, but smaller containers.
GALBA is the short-lived emperor. To our surprise, GALBA is still used. GALBA2 is on his way... #genomeannotation
A screenshot of a template course website with tabs for a syllabus, an assignment guide, slides, and a page on accessibility.
Huge gratitude to the open-source community behind @quarto.org.
With university efforts to improve digital accessibility, it's a great time to switch to Markdown to share class materials in accessible HTML.
Here is my template course website if you want to try it:
judgelord.github.io/PP000/
1/ BRAKER4 hatched!
The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...
What will it be able to do, the magic & shiny BRAKER4? It’s a story of „You asked, we deliver…“ For example, it will distribute across your HPC. It will run repeat masking. It will annotate noncoding RNAs… stay tuned. #genomeannotation
You mean minipoa will fail on shorter, repetitive reads? Definitely not my area of expertise.
github.com/jelber2/mini... uses minimizer_positions from simd-minimizers and is about 1.3 times faster than github.com/henriksson-l...
A POA library, cool stuff. Have you seen this; Minipoa: A minimizer-based method for fast and memory-efficient partial order alignment www.biorxiv.org/content/10.6...
I wonder how much faster and how hard it would be to add simd-minimizers from @curiouscoding.nl and crew
The SquiDBase paper has now been published in NAR Genomics and Bioinformatics: doi.org/10.1093/narg...
SquiDBase (squiggle database) is an open, community-driven resource for raw #nanopore sequencing signal data from #microbial and #viral origin, complemented by corresponding basecalled reads.
Saw this on Twitter/X
AppBundler v1.0 transforms any Julia application into a Snap installer (Linux), MSIX (Windows), or DMG (macOS) without leaving the Julia ecosystem, using cross-platform utilities compiled via Yggdrasil.
#JuliaLang
discourse.julialang.org/t/ann-appbun...
Ok, now that is one heck of a plotting library!
Cooking up a cool feature for kuva with --interactive, where it adds a search, and group highlighting and coordinates on mouse, all within the native SVG file, when looking at it with a browser. This is just the minimal working prototype. What do you think?
Can't you just use the AGC to extract each one by one to build the de Bruijn graph? Just need a lot of storage I guess.
You can convert the rGFA to FASTA? There is also github.com/lh3/OpenHGL?... but in Heng Li's ropebwt3 format. Maybe it can output something too? @lh3lh3.bsky.social any ideas?
Did anybody build a De Bruijn graph on HPRCv2 yet?
I'd like to try running sassy against the Eulertigs of the k=31 graph.
I see the AGC file is only 3GB, so maybe that allows for an easy way to just get an SPSS out of it?
Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social
Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.
rdcu.be/famFj
Open-source, Hardware-Independent GPU Acceleration for Scalable Nanopore Basecalling with Slorado and Openfish www.biorxiv.org/content/10.64898/2026.03...
