Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

DynamicDemiLog: A Single Sketch for Ultrafast Similarity, Frequency, and Cardinality Estimation https://www.biorxiv.org/content/10.64898/2026.06.12.731986v1

The US Navy is using @nanoporetech.com sequencers in the field. www.wadsworth.org/news/wadswor... and defence--blog-com.cdn.ampproject.org/v/s/defence-... #nanopore

Is @nanoporetech.com hac v6 better than 5.2.0 sup? The short answer is no. But are a few errors in a genome worth 5 times more basecalling compute? github.com/Kirk3gaard/M...

Nanopore sequencing provides not just long reads, but the the raw signal data can also be used to identify RNA and DNA modifications. This repository (and the associated review) lists some of the great tools that have been developed www.cell.com/trends/genet...

Hey #genomics and #bioinformatics community: I need an "endorsement" in order to submit a preprint to @arxiv.bsky.social 😭 I'm registered, but can't submit our preprint to q-bio\GN (Genomics) section until we get an endorsement from an existing arXiv author w/endorse privileges. that you? plz DM me🙏

I've been working an a small Julia library for working with raw nanopore sequencing signals. It's still under development and not very mature, but maybe someone may find it useful and want to experiment with it. It provides functionality for signal-to-sequence alignments, basic signal scaling […]

NBD-VRAM Provides Swap Space On Your NVIDIA GeForce GPUs - https://www.phoronix.com/news/NVIDIA-NBD-VRAM

github.com/sstadick/str... Stay in the code. Avoid context switching. That was the whole goal of this endeavor. I wanted to be able to use agents for things like search, one-off questions, and small patches without stepping out as abstracted as something like claude. github.com/sstadick/str...

I updated Learning Zig to work with 0.16 www.openmymind.net/learning_zig/ #Ziglang

Come to ONT's industry event at ASM to hear about two exciting new tools from @jimshaw.bsky.social! SNPmers (polymorphic kmers) are leveraged for impressive performance in both myloasm (metagenomic assembly) and savont (16S ASVs). Registration link 👇

Memory-safe high-performance sequence mapping with rammap https://www.biorxiv.org/content/10.64898/2026.05.26.726289v1

SPLICECRAFT v1.0 IS LIVE!!!!!!!!!!!! Open your terminal and type in "pipx install splicecraft" if you want to try it out, then spam "splicecraft update" often as I push updates frequently. A labor of love for the community I adore. Enjoy! 💚

Awesome idea, bridging Excel with ggplot2 ⬇️ Figra: A WebAssembly-based Excel Add-in for publication-quality scientific visualization with ggplot2 by Yoshiaki Sato: www.biorxiv.org/content/10.6...

A love letter to @nanoporetech.com pod5lib for reading and writing wire compatible pod5 files in Rust. Compared to the python/C++ library with 50k reads it is: - Read: 1.9 faster and uses ~60x less RAM - Write: 1.7x faster and uses ~5x less RAM github.com/Psy-Fer/pod5... crates.io/crates/pod5lib

Interesting that bun now shows up in @rusttrending.bsky.social

Rust was released 11 years ago today. Happy Birthday, Rust! blog.rust-lang.org/2015/05/15/R...

Tried it out this morning. It works! I made this phylogeny using Arabidopsis WUS as the query, against a Kalanchoe genome I am working on. The tree reflects known relationships between WUS and WOX paralogs.

Benchmarking long-read simulators against Oxford Nanopore whole-genome sequencing data https://www.biorxiv.org/content/10.64898/2026.05.06.723380v1

Does anyone know if there's written documentation on how ONT put together their dorado bacterial polishing model? I know it fares well on benchmarks, but what is it based on and how did they put it together? Is anyone testing alternate polishing models these days? 💻🧬🧪

My TEDx talk is online youtu.be/XX0pgmV1_YA?... I talk about using detected species to infer undetected species in #eDNA!

NanoLabel: A fast and accurate real-time nanopore signal classifier https://www.biorxiv.org/content/10.64898/2026.05.03.722500v1

sourceforge.net/projects/bbm... Brian Bushnell and Colleagues are developing DynamicDemi Log methods to rapidly compare genomes instead of more traditional MinHash-like methods. See newer versions of BBMap such as version 39.83 #bbmap #bbtools

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