HERRO has been published in @nature.com nature.com/articles/s41.... This achievement is a result of the great work by Dominik Stanojevic, with contributions from Dehui Lin, @sergeynurk.bsky.social, and Paola Florez de Sessions Welcome to the era of high-quality genome assemblies supported by AI.

Today's pysam 0.24.0 release bundles htslib, samtools, and bcftools 1.23.1 and has pre-built wheels for Python 3.8 through 3.14. Notably it includes modified_bases fixes thanks to reports by Leszek Pryszcz and Jun Mencius, and new documentation for VariantRecord et al written by @timd.one. 🧬🖥️

#JuliaLang RustCall.jl is out! github.com/AtelierArith...

I took a look at how the new(ish) lr:hq preset in minimap2 impacts variant calling—i.e., if I should move to using it instead of the default map-ont for recent ONT data. mbhall88.github.io/post/minimap...

Just released mori 0.1.0 on CRAN — a new R package for shared memory across processes. Parallel R no longer has to mean duplicating your dataset in every worker's RAM. opensource.posit.co/blog/2026-04... 🧵 1/3

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...

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...

Quick taxonomic assignment of Nanopore metabarcoding data

What about Computeral Bioinfology?

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

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

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?

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 https://www.biorxiv.org/content/10.64898/2026.03.25.714356v1

videocardz.com/newz/hp-unve... wow, 4 Nvidia RTX Pro 6000 Blackwell GPU support. Future Oxford Nanopore attachment for the P48 sequence? @kirk3gaard.bsky.social

aq: a jq-like tool to query table-oriented data files. Supports Apache Arrow, Parquet, CSV and NDJSON. Written in #RustLang by my friend @anaethelion.bsky.social github.com/Anaethelion/aq

Simon Ambrozak, Ulysse McConnell, Bhargav Srinivasan, Burak Ozkan, Can Firtina: CERN: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models https://arxiv.org/abs/2603.20420 https://arxiv.org/pdf/2603.20420 https://arxiv.org/html/2603.20420

Ever receive a BAM aligned to “GRCh38” and realize that could mean several different references? We just released ref-solver, a tool that identifies the reference genome behind BAM/CRAM/FASTA files by comparing sequence dictionaries to known builds. 🔗 whatsmygenome.fulcrumgenomics.com Read more 👇

🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳 The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.). See github.com/snakemake/sn... for more

Single-Platform Nanopore Sequencing Enables Diploid Telomere-to-Telomere Genome Assembly and Haplotype-Resolved 3D Chromatin Maps https://www.biorxiv.org/content/10.64898/2026.03.19.712851v1

Hierarchical genomic feature annotation with variable-length queries https://www.biorxiv.org/content/10.64898/2026.03.15.711907v1

HGVS parsing sounds straightforward until you run it at scale across real clinical variants. We just released ferro-hgvs, a Rust-based parser/normalizer that processes millions of variants per second & handles many tricky edge cases other tools struggle with. 🔗 hgvs.acgt.bio Details in blog post👇

Will 2026 be the year we finally see something new from @nanoporetech.com or are we stuck due to the clinical focus? Next generation ASIC chips would be the opportunity to align product lines. One flowcell to rule them all?

OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing https://www.biorxiv.org/content/10.64898/2026.03.18.709804v1

the codex desktop app was only available as a Mac DMG. A while ago, I downloaded it and told codex cli to make it work on linux. It did. Now I use that nearly exclusively. gist.github.com/brentp/b6bd8...

Transformer-based AI has boosted @nanoporetech.com sequencing accuracy, but at a cost to portability due to GPU demands. Our new work, spearheaded by Sara Bakic, introduces Campolina link.springer.com/article/10.1... to improve nanopore signal segmentation for event-based mappers.

Someone ported Karpathy's microGPT to pure #julialang in 99 lines with 0 dependencies, it's 1600x faster than CPython... hard to emphasize enough how impressive this is www.reddit.com/r/Julia/s/Vg...

This looks really interesting and perhaps might enable faster overlapping for HERRO @msikic.bsky.social , not sure academic.oup.com/bioinformati... , also not sure Rawsamble can overlap repetitive sequences, for which minimap2 can, but seems to slow down a lot compared to default settings

Introducing kuva: A scientific plotting library in rust, along with cli binary with the option to plot directly into the terminal. Feel free to drop me some feedback as an issue on the repo github.com/Psy-Fer/kuva crates.io/crates/kuva/...

Vibe coding as a term was coined I think in February 2025, and I saw a job posting looking for someone with 2+ years in vibe coding experience. I know that people were vibe coding with large language models before the term existed but give me a break.

www.biorxiv.org/content/10.6... Clair3 v2 for #nanopore reads, it keeps getting better!

Looks interesting...https://www.biorxiv.org/content/10.64898/2026.02.12.705514v1 Skiver: Alignment-free Estimation of Sequencing Error Rates and Spectra using (k, v)-mer Sketches

Hare 0.26.0 Released - Loop values and for..else - #DragonflyBSD support - Explicit syntax for ignoring errors when needed - Replacing @offset with fields named _ for padding structs - Support for explicitly uninitialized variables harelang.org/blog/2026-02... #HareLang

From @narjournal.bsky.social #NARCriticalReviewsAndPerspectives | Unlocking the full potential of #nanopore sequencing: tips, tricks, and advanced data analysis techniques | #Bioinformatics #Genomics #OpenScience #NGS #OxfordNanopore 🧬 🖥️🧪🔓 ⬇️ academic.oup.com/nar/article/...

Took me way too long to realize that its super easy to just merge pdfs in R rather than fussing with Adobe #rstats library(pdftools) pdf_combine( input = c("file1.pdf", "file2.pdf"), output = "merged.pdf" )

@kirk3gaard.bsky.social , who wants to benchmark @nanoporetech.com 's Dorado with a Nvidia 5090 drawing 2500W? "MSI made a 2500W limited-edition RTX 5090 with a screen, because why not?"

Want a quick way to check #ziglang versions? I've published a tool that shows the latest Zig release + all versions at a glance, with links to release notes, docs, and downloads. mathias.blog/tools/whatzi...

I made a small wrapper library for reading slow5/blow5 files in #julialang based on the C slow5lib. If anyone working with #Nanopore sequencing is interested, you can find it here: https://codeberg.org/mzdravkov/Slow5.jl

Kraken 2 (K2) community: we are giving more attention to our new `k2` wrapper, and a NEW functionality since 2.17.0 is: you can build several component K2 indexes, e.g. each covering a different Refseq database, and then query them all at once... github.com/DerrickWood/... 1/6