From @robert.bio @helenechiapello.bsky.social @mthomaschollier.bsky.social & col. in @plos.org #Computational #Biology | Training biologists in #Unix command-line skills: From curriculum to interactive online tutorials|#Education #OpenEducationalResources | ๐ฅ๏ธ ๐งช
โฌ๏ธ
journals.plos.org/ploscompbiol...
Host read removal sounds simple. It's not. ๐งซ
Ep. 151 of #microbinfie: we talk with @bede.im about Deacon โ 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...
Just finished teaching another semester of Genomic Data Visualization! ๐ฅณ
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...
Wow, this is amazing @wytamma.bsky.social!
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".
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:
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3D printed magnetic bead contraptions
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When sequencing more is easier than sequencing less
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Bread machine analogies
Playing with sandbox.bio. This was remarkably cathartic.
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.
๐ Our new paper on Alignoth just published in Bioinformatics!
Alignoth generates self-contained interactive HTML read alignment plots from BAM files โ Rust-based, portable, and ideal for headless workflows.
๐ doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
Blogpost: I took an oral probiotic for a month and did microbiome sequencing at @Plasmidsaurus.
blog.booleanbiotech.com/oral-microbi...
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!
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...
Indeeeeed ๐
You can also use 42basepairs to view public buckets and preview file contents e.g. 42basepairs.com/browse/s3/op... ๐
One last bioinformatics puzzle before the holidays: Can you figure out the file formats of unlabeled sequence data? ๐
sandbox.bio/puzzles/form...
These are fun educational puzzles to improve debugging skills of students! thanks to @robert.bio for creating these
sandbox.bio/puzzles
We are thrilled to announce the first official release (v0.1.8) of #๐ฏ๐ฒ๐ฑ๐ฑ๐ฒ๐ฟ, the successor to one of our flagship tool, #๐ฏ๐ฒ๐ฑ๐๐ผ๐ผ๐น๐! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
I'm building out a new section on sandbox.bio with debugging puzzles that could be relevant: sandbox.bio/puzzles
I didnโt realize yโall got Rust tools compiled in a biowasm compatible way, thatโs awesome!
Workshop landing page with demos here -> wasmodic.github.io
Hmmm ๐ง
@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#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
Excited to announce a new bqtools tutorial on sandbox.bio by @noamteyssier.bsky.social! Learn about the BINSEQ file format, and how it can replace FASTQ files for better data compression and faster parallel processing: sandbox.bio/tutorials/bq...
BINSEQ is a high-performance format for sequencing data and bqtools is a CLI tool that lets you create and manipulate these files in the style of samtools.
Excited to release a tutorial with @robert.bio showcasing how to use it to encode, decode, and grep sequences in the browser on sandbox.bio!
Interested in learning materials to prepare undergraduate students for working with pathogens and pathogen data? Iโm hosting a small curriculum development sprint/workshop. Industry/clinical and educators needed.
Please share. Apply by November 28, 2025
dnalc.cshl.edu/pdn-2026-wor...
Students often ask me how to get bioinformatics experience, and I say "projects, projects, projects!". And inevitably they say "okay but how do I find a project to do?". So I made this video with 15 project ideas:
www.youtube.com/watch?v=dfJK...
Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#
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/....
Ah, by sorting the matrix, I meant sorting the set of 9 strings defined by each row of the matrix, not sorting the 2 strings defined by each column of the matrix.
Oh wow, BWT in a Google Sheet, thatโs awesome!
This is wonderful to play with, highly recommended for anyone who wants to understand the BWT