Noam Teyssier

The workspace publishing has been such a hassle. So glad to see this out

Sounds great! Would be very interested in that and happy to help build one

bsky.app/profile/noam...

Here was a benchmark I ran a while back comparing twobit and binseq on a single-thread

2bit was built for genomes where there are very long contiguous N-blocks. the overhead for managing these blocks though on fastq-style records (generally very short and non-contiguous Ns) is massive and most of the time unnecessary.

Paraseq 0.4 is out now! With double the throughput for processing paired-end input :)

github.com/noamteyssier...

Added a feature to bqtools yesterday for colored grep output. Also supports colored FASTX output as well. Already useful this morning as I troubleshoot some sequencing outputs!

CRISPR screening by AAV episome-sequencing (CrAAVe-seq): a scalable cell-type-specific in vivo platform uncovers neuronal essential genes - Nature Neuroscience The authors developed an adeno-associated virus-based high-throughput in vivo CRISPR screening platform for endogenous mouse brain cell types. Using this platform, they define genes and pathways essen...

Excited that the paper presenting our mouse brain in vivo CRISPR screening platform is out today in @natneuro.nature.com!

Great team effort, led by Biswa Ramani and @ivlrose.bsky.social in the Kampmann lab.

www.nature.com/articles/s41...

Accelerating k-mer-based sequence filtering The exponential growth of global sequencing data repositories presents both analytical challenges and opportunities. While k - mer-based indexing has improved scalability over traditional alignment fo...

Preprint alert!
We present K2Rmini, an ultra-fast, grep-like tool that extracts sequences of interest from FASTA/FASTQ files based on their k-mer content.
www.biorxiv.org/content/10.1...
A thread

Writing in rust again after a long stretch of python is such a breath of fresh air.

Are you going to have a remote component to this? Would love to watch some of these talks if I can

Ah this is the way that I do it in paraseq! Doesn't work for fastq headers but works well for fasta

Introducing Arc Institute’s first virtual cell model: STATE

Downloaded more for business, or pleasure? This mini-project was inspired by this tweet: After which I spent about two hours making a small script that grabs data from the rust package repository crates.io, and analyses the ...

Pretty cool little utility and blog post - fun to see the business/pleasure index for rust crates

boydkane.com/projects/cra...

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment.
arxiv.org/abs/2506.12986

R.I.P your email inbox haha

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon

ish is a grep-like CLI tool that uses optimal alignment instead of exact matching.

It’s record-type aware, supporting line, FASTA, and FASTQ records.

Built in Mojo as a proof of concept for bioinformatics.

🧵1/5

Bon Next-gen compile-time-checked builder generator, named function's arguments, and more!

A good workaround for defaults I use sometimes is Bon. Adds to compile times though which can be annoying

bon-rs.com

lol what expires in this? It’s like pure metal

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

Love seeing audio stuff in rust. How’d you make the visualization?

📜 Excited to share insights from our recent paper: "Kaminari: a resource-frugal index for approximate colored k-mer queries". The study aims to efficiently identify documents containing a query string, focusing on DNA strings. www.biorxiv.org/content/10.1... 🧬 🖥️ 1/8

One of the great success stories of change haha

I think the best way to spur change is to make the new solution as easy as the old one. If it's an easy swap then I think its people will try it out and convince themselves its worth it.

Like swapping out std::collections::HashMap for hashbrown::HashMap.

But its easier said than done

Oftentimes inertia is the biggest reason for lack of change. If things work as they are people are unlikely to change.

Cell simulation as cell segmentation - Nature Methods Proseg is a segmentation approach for single-cell spatially resolved transcriptomics data that uses unsupervised probabilistic modeling of the spatial distribution of transcripts to accurately segment...

Our Proseg paper is now out in Nature Methods!
www.nature.com/articles/s41...

We borrowed a sampling procedure from the cell simulation literature to infer cell boundaries that best explains the spatial distribution of transcripts.

lofi Archive radio 🎞️ beats to scan/read microfiche to YouTube video by Internet Archive

📄 The scanners are humming, the film is flowing.

The microfiche livestream is up—digitizing government docs in real time for Democracy’s Library.

Perfect second-screen vibes: Preservation in progress.

🕢 Live M-F, 7:30am–3:30pm PT (except U.S. holidays)
➡️ www.youtube.com/live/aPg2V5R...

So yeah, this is why I keep going on about: do we have to sanitize user input or not? File formats where bad inputs are simply not representable are good, because it saves us from this 100x slowdown.

One other option I’d be curious about is an unreachable!()

I feel like -1 would lead to some smaller assembly footprint… but super curious what the diff is