iiinova — where your digital self keeps evolving

Brent Pedersen @brent-p.bsky.social · 01/09/2026

a new release of somalier with a user fix for long reads: github.com/brentp/somal... somalier continues to get better and if you're not using it or another means to detect sample swaps, you're operating blind reach out to me for consulting if you want to do some in *depth* QC on large cohorts

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Brent Pedersen @brent-p.bsky.social · 14/08/2026

"load-bearing" is coming up a lot lately. Anyone seen a sort of LLM etymology of how these phrases come to be so commonly-used? Doesn't seem obvious how this happens with RL as I understand it. And to obviate the obvious response: "you're right to call that out!"

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James Ferguson @psy-fer.bsky.social · 29/07/2026

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...

openai.com

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.

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Seth Stadick @ducktapeprogrammer.bsky.social · 28/07/2026

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?

biodatageeks.org

Interval operations benchmark — update September 2025 - polars-bio

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Seth Stadick @ducktapeprogrammer.bsky.social · 28/07/2026

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.

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Brent Pedersen @brent-p.bsky.social · 15/05/2026

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

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Brent Pedersen @brent-p.bsky.social · 06/05/2026

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/...

brentp.github.io

AI Scripting - Brent Pedersen

Scripting interfaces help users.

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Brent Pedersen @brent-p.bsky.social · 30/04/2026

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

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Brent Pedersen @brent-p.bsky.social · 17/04/2026

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.

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Brent Pedersen @brent-p.bsky.social · 15/04/2026

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)

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Brent Pedersen @brent-p.bsky.social · 12/03/2026

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...

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Brent Pedersen @brent-p.bsky.social · 12/03/2026

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.

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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 12/03/2026

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...

docs.google.com

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...

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Brent Pedersen @brent-p.bsky.social · 05/03/2026

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.

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Brent Pedersen @brent-p.bsky.social · 05/03/2026

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...

chatgpt.com

ChatGPT - bedder

help with bedder commands and python snippets

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Brent Pedersen @brent-p.bsky.social · 22/02/2026

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)

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Brent Pedersen @brent-p.bsky.social · 30/01/2026

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

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Brent Pedersen @brent-p.bsky.social · 23/01/2026

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.

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Brent Pedersen @brent-p.bsky.social · 14/01/2026

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.

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Brent Pedersen @brent-p.bsky.social · 12/01/2026

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.com

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

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Brent Pedersen @brent-p.bsky.social · 30/12/2025

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

brentp.github.io

AI Coding - Brent Pedersen

Writing real software with AI coding tools

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Brent Pedersen @brent-p.bsky.social · 28/12/2025

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...

brentp.github.io

Calendar

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Brent Pedersen @brent-p.bsky.social · 28/12/2025

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?

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Brent Pedersen @brent-p.bsky.social · 22/12/2025

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...

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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 02/12/2025

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.

github.com

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 ...

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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 02/12/2025

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

quinlanlab.org

Intro to Bedder – The Quinlan Lab

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Brent Pedersen @brent-p.bsky.social · 18/11/2025

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

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Brent Pedersen @brent-p.bsky.social · 06/11/2025

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

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Rob Patro @robp.bsky.social · 06/03/2025

This is very cool work and I'm happy to see it published. Vcfexpress by @brent-p.bsky.social and @aaronquinlan.bsky.social allows building (essentially) arbitrary VCF filters expressed in lua code with parsing & eval powered by rust! academic.oup.com/bioinformati...

academic.oup.com

Vcfexpress: flexible, rapid user-expressions to filter and format VCFs

AbstractMotivation. Variant Call Format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequ

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Brent Pedersen @brent-p.bsky.social · 04/02/2025

vcfexpress applies simple user expressions variants in a VCF. it can replace one-off python scripts to manipulate VCFs, likely with better performance. we'd like to collect use-cases here: github.com/brentp/vcfex... if you have a use-case and want some pointers, open an issue

github.com

vcfexpress/examples at main · brentp/vcfexpress

expressions on VCFs. Contribute to brentp/vcfexpress development by creating an account on GitHub.

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Brent Pedersen @brent-p.bsky.social · 28/01/2025

vcfexpress is a command-line tool built in rust that lets users apply lua expressions to modify or filter a vcf from the command-line github.com/brentp/vcfex... new release with better docs github.com/brentp/vcfex... and examples github.com/brentp/vcfex...

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Brent Pedersen @brent-p.bsky.social · 27/01/2025

I am looking for a mentor for the rust programming language. My latest issue is with trait bounds (github.com/brentp/simpl...) but I have a few things I generally hit. I can compensate with $$ or interesting problems. :) Please share with relevant people and feel free to DM.

github.com

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Brent Pedersen @brent-p.bsky.social · 25/11/2024

with Jason K from @aaronquinlan.bsky.social lab, I have been dusting off fraguracy, which evaluates sequencing error rates using the portion of bases from paired end reads that overlap. New release adds, among other niceties, tracking for distance to homopolymers github.com/brentp/fragu...

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