I was recently invited to provide a case study along with other researchers for this blog post+pre-print. My main points are: AI agents are useful, but steering through expertise, verification, responsibility, and support are more important than ever openai.com/index/scient...

Scientific computing in the age of agentic AI

A new field report shows how scientists use AI coding agents to modernize scientific computing, accelerating software development and discovery in genomics and beyond.

openai.com

I have some large changes queued up for rust-lapper to address the worst-case in these benchmarks: biodatageeks.org/polars-bio/b... BUT, it's now a fundamentally different data structure. The API is the same for using it. Do I release as a v2 of rust-lapper, or release as a brand new crate?

Interval operations benchmark — update September 2025 - polars-bio

biodatageeks.org

The speedups roughly 1.5x faster on the general cases and ~76x faster on the worst case in that benchmark post. Lapper as an idea originates from @brent-p.bsky.social, and a large part of its uniqueness is how simple it is.

thehackernews.com/2026/05/mini... It's hard to find all these in one place: ~/.npmrc min-release-age=7 ~/.config/uv/uv.toml exclude-newer = "7 days" ~/.bunfig.toml [install] minimumReleaseAge = 604800 ~/.config/pnpm/config.yaml minimumReleaseAge: 10080

LLMs open up the possibility of providing more functionality and customization for command-line tools and anything that takes a config without drowning users by exposing a scripting interface. That's basically it, but a bit more here: brentp.github.io/latest/blog/...

thanks to @ankane.bsky.social echtvar is now available in brew: brew install echtvar dat is superleuk!

Brent Pedersen@brent-p.bsky.social · 3mo ago

With help from contributors, echtvar is still improving: github.com/brentp/echtvar

With help from contributors, echtvar is still improving: github.com/brentp/echtvar

github.com/brentp/blamm... Does QC and EDA for long reads. It was written entirely by LLM.

GitHub - brentp/blammo-qc: quick qc on long-read alignment files. Show read-length and depth distributions

quick qc on long-read alignment files. Show read-length and depth distributions - brentp/blammo-qc

github.com

New version of somalier is up: github.com/brentp/somal... Has a CHARR contamination estimator, a CONPAIR pair-wise inter-sample contaminatoin estimator, an AB/depth plotter and other improvements to make it of greater utility in cancer samples.

Brent Pedersen@brent-p.bsky.social · 4mo ago

the next version will have better contamination estimates (CHARR-like) and pairwise contamination (CONPAIR-like) and concordance of homozygous sites. It will also have a tool to plot sketches like this as interactive html where we can see large chromosomal events.

as part of my work with isabl genomics, I've been updating somalier with more info for cancer samples (contamination and concordance). somalier extracts small "sketches" of ~20K sites from a BAM/CRAM/VCF and then does rapid all-vs-all kinship checks. (1/n)

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...

Again, I think making a custom GPT (or similar) as I did for bedder will be the default for most software shortly. If it can't answer common questions, improve the docs and refresh and the maintenance burden of answering user questions goes down.

Aaron Quinlan (he/him)@aaronquinlan.bsky.social · 5mo ago

Brent Pedersen, Mitchell Vollger and I have "posted" our preprint of the manuscript describing bedder, a complement to the functionality of bedtools. The "preprint server" we have chosen is google docs because it was rejected by biorxiv. docs.google.com/document/d/1...

Brent Pedersen, Mitchell Vollger and I have "posted" our preprint of the manuscript describing bedder, a complement to the functionality of bedtools. The "preprint server" we have chosen is google docs because it was rejected by biorxiv. docs.google.com/document/d/1...

bedder-manuscript.v10

Bioinformatics, 2026, 0–0 doi: 10.1093/bioinformatics/xxxxx Advance Access Publication Date: DD Month YYYY Genome Analysis Genome Analysis bedder: flexible genome interval intersection with user-defi...

docs.google.com

I would guess that soon, every tool will have one of these. It is more interactive than just documentation and better than waiting for a grumpy maintainer to answer the same question in a github issue or personal email.

Brent Pedersen@brent-p.bsky.social · 5mo ago

Feeding my markdown docs to this, then using it in anger shows where the docs need to be bolstered and provides a nice reference for users: help.openai.com/en/articles/... here's one for bedder: chatgpt.com/g/g-69a6027f...

Feeding my markdown docs to this, then using it in anger shows where the docs need to be bolstered and provides a nice reference for users: help.openai.com/en/articles/... here's one for bedder: chatgpt.com/g/g-69a6027f...

I had a similar, less principled way of doing this, but this does seem to work quite well after trying a couple of large changes with it: boristane.com/blog/how-i-u... (I use codex, but same idea)

AGENTS.md > skills vercel.com/blog/agents-...

scratch that. better to use gemini-cli, turn on preview features and then get gemini 3.0 pro and flash for free for a decent amount each day.

Brent Pedersen@brent-p.bsky.social · 7mo ago

crush coding agent with a free plan from cerebras using glm4.7 model is an easy way to start with coding cli tools. inference-docs.cerebras.ai/support/rate... github.com/charmbracele... crush is static binary that detects your CEREBRAS_API_KEY. GLM 4.7 isn't as good as Opus, but it is very solid.

crush coding agent with a free plan from cerebras using glm4.7 model is an easy way to start with coding cli tools. inference-docs.cerebras.ai/support/rate... github.com/charmbracele... crush is static binary that detects your CEREBRAS_API_KEY. GLM 4.7 isn't as good as Opus, but it is very solid.

another reminder about htsvcf which allows either 1. rust library to support javascript expressions (filtering/modification) on variants from VCF/BCF 2. javascript (node/bun) library for reading/writing/modifying variants from vcf/bcf. both very performant. github.com/brentp/htsvcf

GitHub - brentp/htsvcf: lib for scripting vcf access from rust and node module for vcf access from js/ts

lib for scripting vcf access from rust and node module for vcf access from js/ts - brentp/htsvcf

github.com

a post about how, with LLMs, I wrote a new set of libraries. Wrapping htslib is my hello-world but doing it in rust to allow javascript expressions handled by V8 was more substantial project. The tools and LLMs are now getting quite good: brentp.github.io/latest/blog/... let me know what you think

my LLM-coded version of the single-page year calendar that's been going around. This one can be scripted with javascript to highlight cells, change the borders and texts. It also allows saving and sharing via url: brentp.github.io/single-page-... with code here: github.com/brentp/singl...

so Opus 4.5 is excellent for coding. I've been using these LLMs for coding for a while and it felt like slow improvement with each new model and sometimes more work to guide the model. Opus 4.5 just works. It solves hard problems and has good taste. Anyone else notice this?

I'll write more about this later, but as an experiment in LLM coding (GPT-5.2 and Opus 4.5), I wrote a JS wrapper for rust-htslib to read/write modify VCFs: www.npmjs.com/package/htsvcf works on linux (x64/aarch64) and OSX. brentp.github.io/htsvcf/lates...

Get bedder v0.1.8 and r𝗲𝗮𝗱 𝘁𝗵𝗲 𝗱𝗼𝗰𝘂𝗺𝗲𝗻𝘁𝗮𝘁𝗶𝗼𝗻 here: github.com/quinlan-lab/... We are looking for researchers to kick the tires, integrate bedder into their pipelines, and provide feedback on the Python functions, performance, and overall user experience! Please share and give us your feedback.

Release Release v0.1.8 · quinlan-lab/bedder-rs

Changes in v0.1.8 Downloads bedder-static-linux-x86_64: Static binary for Linux x86_64 (no dependencies required) bedder-static-macos-x86_64-python3.13: macOS x86_64 binary built with Python 3.13 ...

github.com

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

Aardvark? github.com/PacificBiosc...

GitHub - PacificBiosciences/aardvark: A tool for sniffing out the differences in vari-Ants

A tool for sniffing out the differences in vari-Ants - PacificBiosciences/aardvark

github.com

I vaguely recall seeing #bioinformatics tool that could compare variants (or set of variants) using haplotypes rather than simply normalize and check for equality. That murky description is about as specific as I can get. Any pointers? IIRC, it's not just a truth-set evaluation tool. Has API

how do we feel about putting JSON in the INFO field of a VCF?