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Noam Teyssier @noamteyssier.bsky.social · 2d

Have you tried samply?

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Noam Teyssier @noamteyssier.bsky.social · 28d

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

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Noam Teyssier @noamteyssier.bsky.social · 29d

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

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Noam Teyssier @noamteyssier.bsky.social · Sep 15

bsky.app/profile/noam...

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

Noam Teyssier @noamteyssier.bsky.social · May 8

Ah yes 2bit was a big inspiration for binseq - I didn't include it because it wasn't widely used and it was more geared towards large genomes so I figured it wouldn't scale.

But you're right I didn't formally test it. Here's a simple bench with Kent's utils (1-core bqtools to be fair)

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Noam Teyssier @noamteyssier.bsky.social · Sep 15

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.

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Reposted by Noam Teyssier

Ragnar {Groot Koerkamp} @curiouscoding.nl · Sep 4

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

github.com/noamteyssier...

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Noam Teyssier @noamteyssier.bsky.social · Sep 4

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!

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Reposted by Noam Teyssier

Martin Kampmann @kampmann.bsky.social · Aug 22

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...

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...

www.nature.com

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Reposted by Noam Teyssier

Antoine Limasset @npmalfoy.bsky.social · Jul 2

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

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...

www.biorxiv.org

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Noam Teyssier @noamteyssier.bsky.social · Jun 26

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

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Noam Teyssier @noamteyssier.bsky.social · Jun 26

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

Noam Teyssier @noamteyssier.bsky.social · Jun 24

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

Reposted by Noam Teyssier

Arc Institute @arcinstitute.org · Jun 23

Introducing Arc Institute’s first virtual cell model: STATE

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Noam Teyssier @noamteyssier.bsky.social · Jun 18

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

boydkane.com/projects/cra...

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 ...

boydkane.com

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Reposted by Noam Teyssier

Heng Li @lh3lh3.bsky.social · Jun 17

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

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Noam Teyssier @noamteyssier.bsky.social · Jun 16

R.I.P your email inbox haha

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Reposted by Noam Teyssier

Bede Constantinides @bedec.bsky.social · Jun 13

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

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jun 13

Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1

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Reposted by Noam Teyssier

Seth Stadick @ducktapeprogrammer.bsky.social · Jun 9

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

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jun 9

Ish: SIMD and GPU Accelerated Local and Semi-Global Alignment as a CLI Filtering Tool https://www.biorxiv.org/content/10.1101/2025.06.04.657890v1

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Noam Teyssier @noamteyssier.bsky.social · Jun 8

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

bon-rs.com

Bon

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

bon-rs.com

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Noam Teyssier @noamteyssier.bsky.social · Jun 7

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

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Reposted by Noam Teyssier

Rayan Chikhi @rayanchikhi.bsky.social · Jun 3

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

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Noam Teyssier @noamteyssier.bsky.social · May 28

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

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Reposted by Noam Teyssier

Pierre Peterlongo @pierrepeterlongo.bsky.social · May 27

📜 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

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Noam Teyssier @noamteyssier.bsky.social · May 23

One of the great success stories of change haha

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Noam Teyssier @noamteyssier.bsky.social · May 23

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

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