iiinova — where your digital self keeps evolving

Reposted by Robert Aboukhalil

Samuel Lampa @smllmp.bsky.social · 25/09/2026

New blog: Emu runs an order of magnitude faster for high quality (sup) R10 @nanoporetech.com 16S data, with the lr:hq preset for minimap2, in addition to improving downstream analysis as previously blogged by @mbhall88.bsky.social: livingsystems.cc/posts/lrhq-s... #bioinformatics #microbinfie

Bar graph showing how Emu with the lr:hq preset is running ca 10 times faster than with map-ont, for three different data sizes: 1k, 5k and 10k reads.

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Robert Aboukhalil @robert.bio · 27/08/2026

AI CEOs keep predicting the end of disease, while pharma CEOs have a much more thoughtful take on how AI is actually speeding up the drug development timeline: youtu.be/ukZvIjq2oJc

youtu.be

Will AI cure all disease in 10 years?

YouTube video by OMGenomics

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Robert Aboukhalil @robert.bio · 14/08/2026

You can now embed a Sandbox Bio terminal in your own website or GitHub Pages! Just add a script tag and your website gets a terminal at the bottom of the page, and you can customize which files are preloaded in there: sandbox.bio/training/embed

sandbox.bio

Embed sandbox.bio

Embed a live sandbox.bio terminal directly in your website or blog post.

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Robert Aboukhalil @robert.bio · 13/08/2026

I made a Nextflow tutorial you can run from your browser!! Nothing to install, and cloud costs are sponsored by @carolinacloud.io You build a pipeline to find how much sequencing you need to detect Listeria in ice cream, with interactive challenges along the way. sandbox.bio/tutorials/ne...

sandbox.bio

Introduction to Nextflow

Interactive Nextflow tutorial: write your first pipeline and run it on real cloud infrastructure, for free and with no installation. Also learn to use existing nf-core pipelines.

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Robert Aboukhalil @robert.bio · 12/08/2026

Today, Sandboxbio is releasing an interactive companion to @carpentries.carpentries.org's excellent Python workshop 🐍 From your browser, you write and run Python code to solve the exercises, with hints and instant feedback. carpentries.org/blog/2026/08...

carpentries.org

Interactive Carpentries exercises on sandbox.bio

Sandbox.bio is a free bioinformatics training platform, where all the tools you need run in the browser, so no setup is needed. This week, Sandbox.bio is releasing Programming with Python Exercises, a...

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Robert Aboukhalil @robert.bio · 11/08/2026

Datavzrd is an awesome tool that turns CSVs into shareable reports that can sort/filter/plot your data, made by @fxwiegand.bsky.social and @johanneskoester.bsky.social You can now run Datavzrd in the browser and rebuild the reports in real time as you edit the config: sandbox.bio/playgrounds/...

sandbox.bio

Interactive datavzrd playground

Playground for creating interactive reports from tabular data using datavzrd

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Robert Aboukhalil @robert.bio · 10/08/2026

You can now turn your GitHub repos into sandbox.bio tutorials! You get a shareable URL, where code blocks are runnable, and files are preloaded in the terminal. For example, @benlangmead.bsky.social used this in a recent kraken2 workshop. You can see it in action here: sandbox.bio/training/git...

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Robert Aboukhalil @robert.bio · 06/08/2026

I can't believe it's already been 5 years since I first released sandbox.bio! 🥳 To celebrate, next week we'll release one new feature every day of the week. Follow along at sandbox.bio/anniversary, or here on BlueSky.

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Kai Blin @kblin.bsky.social · 03/08/2026

Great write-up on the work my colleague Xinglin has been doing.

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Reposted by Robert Aboukhalil

Human Pangenome Reference Consortium @humanpangenome.bsky.social · 24/07/2026

Explore the HPRC Year 2 pangenome graph with Graphoscope. Search a gene or genomic region to visualize the pangenome graph at that locus with no pangenome data or specialized setup required. Try it here: marianattestad.github.io/graphoscope/...

marianattestad.github.io

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Robert Aboukhalil @robert.bio · 22/07/2026

grep is a fantastic tool, but it doesn't really work on sequencing data: it breaks when the pattern is in the read name, and doesn't support paired-end FASTQs. Thanks to @nilshomer.com, we have a new interactive guide on using fqgrep to find patterns in FASTQ files: ➡️ sandbox.bio/tutorials/fq...

sandbox.bio

Interactive bioinformatics tutorials

Learn bioinformatics from your browser, no setup required. Everything runs in a sandbox, so you can experiment all you want.

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Reposted by Robert Aboukhalil

Benjamin J. Buchfink @bbuchfink.bsky.social · 13/07/2026

DIAMOND v2.2.4 is available today, providing compositional matrix adjust for the clustering workflows and more. github.com/bbuchfink/di...

github.com

GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.

Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond

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Reposted by Robert Aboukhalil

Bede Constantinides @bede.im · 13/07/2026

Ever wanted to quickly check host content of DNA sequences? bede.im/sapiometer

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Dr Andrew Lonsdale @lonsbio.bsky.social · 10/07/2026

Prompts are available from the corresponding author upon reasonable request.

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Robert Aboukhalil @robert.bio · 02/07/2026

Check out our new Makefile tutorial if you want to finally understand what those "make install" commands actually do when you paste them in your terminal, and how to use them in your work: sandbox.bio/tutorials/ma... Thanks to Stephen J Bush for contributing this tutorial!

sandbox.bio

Intro to Makefiles

Interactive make tutorial: learn to use and create your own Makefile using a command-line interface in your browser.

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Reposted by Robert Aboukhalil

Andrew Carroll @acarroll.bsky.social · 01/07/2026

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

andrewcarroll.github.io

The Best of Both Worlds - Assessing MiniBWA

Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...

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Robert Aboukhalil @robert.bio · 24/06/2026

New on sandbox.bio: a FastQC playground you can use for teaching QC analysis of sequencing data. It runs entirely in the browser, GUI and all (thanks to CheerpJ and WebAssembly!) ➡️ sandbox.bio/playgrounds/...

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Reposted by Robert Aboukhalil

Maria Nattestad 🧬💻 @omgenomics.com · 23/06/2026

Okay I'm sorry if you're all getting tired of it, but here's yet another I-built-this-with-AI post. It is my first time really vibe-coding something, but it's for a good cause: updating my old academic software Assemblytics that I had nearly shut down multiple times due to server issues.

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Reposted by Robert Aboukhalil

Rob Patro @robp.bsky.social · 14/06/2026

salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/

combine-lab.github.io

salmon

Fast, accurate transcript quantification from RNA-seq reads.

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Reposted by Robert Aboukhalil

scverse @scverse.bsky.social · 27/05/2026

scverse conference 2026 will take place in Copenhagen, October 12–14. ✨ Three days of all-things-single-cell and open-source tooling and community in real life. More details soon but for now, mark your calendars. scverse.org/conference20... See you in Copenhagen 🇩🇰

scverse.org

scverse conference 2026

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Reposted by Robert Aboukhalil

Rob Patro @robp.bsky.social · 26/05/2026

This seems like an awesome opportunity for people looking to pick up Rust experience and contribute to a very cool project! I hope for typst to become the standard for writing structured scientific and mathematical documents, saving us from the tyranny of LaTeX and the insanity of Word!

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Reposted by Robert Aboukhalil

Phil Ewels @ewels.bsky.social · 15/05/2026

It was great fun talking to @robert.bio and his edit is great (I love some of the overlays, especially the one about @robp.bsky.social being an authority 😂)

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Robert Aboukhalil @robert.bio · 14/05/2026

I've seen lots of AI rewrites in bioinformatics lately, and I’m concerned because LLMs can be confidently wrong. What do the best tool builders do to make sure their rewrites are correct? How can we tell if a rewrite is flawed? I interviewed 5 scientists to find out: youtu.be/0o2XnEBDxrI

youtu.be

I interviewed 5 bioinformatics experts about AI rewrites

YouTube video by OMGenomics

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Reposted by Robert Aboukhalil

Simon Hammann @simonhammann.bsky.social · 20/04/2026

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

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Reposted by Robert Aboukhalil

Lee Katz @lskatz.github.io · 26/03/2026

Host read removal sounds simple. It's not. 🧫 Ep. 151 of #microbinfie: we talk with @bede.im about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2. #metagenomics on.soundcloud.com/gEm7QyaTauvd...

soundcloud.com

151 - Deacon part 1

In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read

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Reposted by Robert Aboukhalil

Dr. Jean Fan @jef.works · 15/03/2026

Just finished teaching another semester of Genomic Data Visualization! 🥳 This semester, I integrated AI-assisted vibe coding. Some students used AI to excel beyond the mechanics of coding. Others struggled in ways I did not expect. I reflect on my blog: jean.fan/2026/03/15/v...

jean.fan

Jean Fan | Personal site

Personal website of Prof. Jean Fan

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Reposted by Robert Aboukhalil

Albert Vilella, PhD. @albertvilella.bsky.social · 13/02/2026

I saw a Youtube video by @omgenomics.com profiling the work that @plasmidsaurus.bsky.social has been doing in streamlining sample preparation for their Plasmid sequencing and RNA-seq products. Interesting to see @OpenTrons instruments *everywhere*, and how they turn operations "pipette triggers".

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Robert Aboukhalil @robert.bio · 12/02/2026

We just released a video from our visit to @plasmidsaurus.bsky.social, where we spoke with Mark Budde and team: www.youtube.com/watch?v=nS2o... Highlights include: ✅ 3D printed magnetic bead contraptions ✅ When sequencing more is easier than sequencing less ✅ Bread machine analogies

youtube.com

The "Why Not?" Era of Sequencing Has Begun

YouTube video by OMGenomics

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Reposted by Robert Aboukhalil

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 05/02/2026

Playing with sandbox.bio. This was remarkably cathartic.

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Kara Swisher @karaswisher.bsky.social · 25/01/2026

That tech oligarchs are noisy and incensed about the remote possibility of a wealth tax and utterly silent about the murder of a man who was only using the phone they invented to chronicle the thuggish government goon squads should tell you everything about these desiccated souls.

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Felix Wiegand @fxwiegand.bsky.social · 08/01/2026

🚀 Our new paper on Alignoth just published in Bioinformatics! Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows. 📄 doi.org/10.1093/bioi... #bioinformatics #genomics #rust @johanneskoester.bsky.social

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Brian Naughton @btnaughton.bsky.social · 04/01/2026

Blogpost: I took an oral probiotic for a month and did microbiome sequencing at @Plasmidsaurus. blog.booleanbiotech.com/oral-microbi...

blog.booleanbiotech.com

Boolean Biotech

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Reposted by Robert Aboukhalil

Brian Naughton @btnaughton.bsky.social · 30/12/2025

Releasing alignism, a small tool that I have found useful for doing multiple sequence alignment in browser. hgbrian.github.io/alignism/ - The hard work was done by the awesome biowasm team! - Does tree building too - V fast compared to e.g., muscle on EBI - Not tested that much!

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Reposted by Robert Aboukhalil

Andrew Carroll @acarroll.bsky.social · 24/12/2025

I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful. andrewcarroll.github.io/2025/12/23/t...

andrewcarroll.github.io

The Virtual Cell Will Be More Like Gwas Than Alphafold

There has been significant discussion recently on the concept of the “virtual cell.” I want to summarize the key concepts regarding what the field wants from a virtual cell and the challenges we face....

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Robert Aboukhalil @robert.bio · 22/12/2025

One last bioinformatics puzzle before the holidays: Can you figure out the file formats of unlabeled sequence data? 🎅 sandbox.bio/puzzles/form...

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Reposted by Robert Aboukhalil

Sina Majidian @sinamajidian.bsky.social · 05/12/2025

These are fun educational puzzles to improve debugging skills of students! thanks to @robert.bio for creating these sandbox.bio/puzzles

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Reposted by Robert Aboukhalil

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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Reposted by Robert Aboukhalil

Wytamma @wytamma.bsky.social · 29/11/2025

Workshop landing page with demos here -> wasmodic.github.io

wasmodic.github.io

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Rob Patro @robp.bsky.social · 19/11/2025

@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2

github.com

GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing

A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim

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Robert Aboukhalil @robert.bio · 18/11/2025

Excited to announce a new bqtools tutorial on sandbox.bio by @noamteyssier.bsky.social! Learn about the BINSEQ file format, and how it can replace FASTQ files for better data compression and faster parallel processing: sandbox.bio/tutorials/bq...

sandbox.bio

Efficient sequence analysis with bqtools

Interactive bqtools tutorial: learn to analyse sequence data efficiently with BINSEQ files using a command-line interface in your browser.

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Reposted by Robert Aboukhalil

Noam Teyssier @noamteyssier.bsky.social · 14/11/2025

BINSEQ is a high-performance format for sequencing data and bqtools is a CLI tool that lets you create and manipulate these files in the style of samtools. Excited to release a tutorial with @robert.bio showcasing how to use it to encode, decode, and grep sequences in the browser on sandbox.bio!

sandbox.bio

Efficient sequence analysis with bqtools

Interactive bqtools tutorial: learn to analyse sequence data efficiently with BINSEQ files using a command-line interface in your browser.

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Reposted by Robert Aboukhalil

Jason “Obstacle to Progress” Williams @jasonwilliamsny.bsky.social · 11/11/2025

Interested in learning materials to prepare undergraduate students for working with pathogens and pathogen data? I’m hosting a small curriculum development sprint/workshop. Industry/clinical and educators needed. Please share. Apply by November 28, 2025 dnalc.cshl.edu/pdn-2026-wor...

dnalc.cshl.edu

Call for Applications: Pathogen Data CUREs—Curriculum Development Workshop

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Robert Aboukhalil @robert.bio · 24/10/2025

Students often ask me how to get bioinformatics experience, and I say "projects, projects, projects!". And inevitably they say "okay but how do I find a project to do?". So I made this video with 15 project ideas: www.youtube.com/watch?v=dfJK...

youtube.com

15 Bioinformatics Project Ideas

YouTube video by OMGenomics

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Reposted by Robert Aboukhalil

Ben Langmead @benlangmead.bsky.social · 14/10/2025

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#

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Zamin Iqbal @zaminiqbal.bsky.social · 09/10/2025

This is wonderful to play with, highly recommended for anyone who wants to understand the BWT

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Robert Aboukhalil @robert.bio · 09/10/2025

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

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Samuel Lampa @smllmp.bsky.social · 06/10/2025

"Pro tip": If you are in a restricted environment & need quick access to a linux terminal running locally in the browser for some #bioinformatics messing around - check the sandbox.bio terminal playground. Made a bitly link for for convenience: bit.ly/bioterminal

Screenshot of the sandbox.bio playground for running a linux environment in the browser

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