iiinova — where your digital self keeps evolving

Noam Teyssier @noamteyssier.bsky.social · 12/09/2026

I often find pure research to be a lot more like art than science. I understand completely that feeling they describe of wanting to solve a problem to understand it in the same way I like to learn songs just to be able to feel them under my fingers. Journey before destination - right?

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Noam Teyssier @noamteyssier.bsky.social · 09/09/2026

ah la belle epoque francophones des annees 1970s

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Bede Constantinides @bede.im · 18/08/2026

As requested, Deacon 0.17.0 adds BINSEQ CBQ support. CBQ is a binary sequence format by @noamteyssier.bsky.social that’s tiny on disk, fast to decode, and supports Ns. With CBQ, Deacon can filter sequences at >5 Gbp/s on a laptop (faster than uncompressed FASTA) github.com/bede/deacon/...

Comparison of Deacon host depletion throughput for cbq, cba, fasta, fastq and fastq.gz for simulated viral reads, with varying thread counts.

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 22/03/2026

Helicase: Vectorized parsing and bitpacking of genomic sequences www.biorxiv.org/content/10.64898/20…

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 12/03/2026

Sassy2: Batch Searching of Short DNA Patterns www.biorxiv.org/content/10.64898/20…

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asamelson @asamelson.bsky.social · 28/01/2026

After a long review process, I'm excited that our paper is finally in print: www.cell.com/cell/fulltex... TL;DR: We use CRISPR screens in iPSC-derived neurons to find a new tau E3 ligase and a relationship between oxidative stress, the proteasome, and tau proteolytic fragments. More below 👇

cell.com

CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis

CRISPR screens in iPSC-derived neurons reveal that the E3 ubiquitin ligase CRL5SOCS4 ubiquitinates tau, that CUL5 expression is correlated with resilience in human Alzheimer’s disease, and that electr...

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Arc Institute @arcinstitute.org · 22/01/2026

Arc bioinformatics scientists @noamteyssier.bsky.social and Alex Dobin have just released cyto, an ultra-high throughput processor specifically optimized for @10xgenomics.bsky.social Flex single-cell data. We are excited to make this resource open source: www.biorxiv.org/content/10.6...

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Noam Teyssier @noamteyssier.bsky.social · 22/01/2026

cyto is free, open-source, and production-ready. Built in Rust for reliability at scale. Currently supports 10x Flex GEX and CRISPR, with more modalities coming. Try it out and let us know how it works for you! github.com/ArcInstitute...

github.com

GitHub - ArcInstitute/cyto: A mapper for single cell sequencing reads with abstract geometries

A mapper for single cell sequencing reads with abstract geometries - ArcInstitute/cyto

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Noam Teyssier @noamteyssier.bsky.social · 22/01/2026

cyto is the first large-scale bioinformatics project to build with BINSEQ. Switching to BINSEQ can achieve mapping rates of 50M reads per second reduce your storage requirements by about 40%. github.com/ArcInstitute...

github.com

GitHub - ArcInstitute/binseq: A high efficiency binary format for sequencing data

A high efficiency binary format for sequencing data - ArcInstitute/binseq

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Noam Teyssier @noamteyssier.bsky.social · 22/01/2026

We also show that we can reproduce the results of CellRanger at a fraction of the resource cost. Our concordance is above 99.85% as measured via Spearman on matched cell UMIs and our lower-dimensional representations show perfect overlap with no method specific clustering.

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Noam Teyssier @noamteyssier.bsky.social · 22/01/2026

cyto was built from the ground up to be modular and to expose the individual modules to the user. Each step is highly optimized and can be run independently, perfect for production scale workflows as it allows for better parallelization and resource allocation on smaller nodes

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Noam Teyssier @noamteyssier.bsky.social · 22/01/2026

Currently the only tool that supports this data type is CellRanger and we show that cyto provides runtimes an order of magnitude faster (16x), uses less than half the memory, dramatically reduces CPU-hours (30x) and reduces total IO by more than 5x.

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Noam Teyssier @noamteyssier.bsky.social · 22/01/2026

Today I’m happy to release cyto, a tool I’ve developed at @arcinstitute.org to dramatically increase our computational throughput with 10x-flex single-cell processing by more than 16X!

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Noam Teyssier @noamteyssier.bsky.social · 21/01/2026

I've tried this at least 3 times haha I think honestly the best way to do it is not really to port it but drastically rework the way that its written.

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Noam Teyssier @noamteyssier.bsky.social · 09/01/2026

Maybe this will be the year we start to really question the foundational infrastructure of the field. Obligatory BINSEQ mention here - keep a lookout the next couple weeks for an update! github.com/arcInstitute...

github.com

GitHub - ArcInstitute/binseq: A high efficiency binary format for sequencing data

A high efficiency binary format for sequencing data - ArcInstitute/binseq

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Noam Teyssier @noamteyssier.bsky.social · 09/01/2026

It is the year 2026 - bioinformaticians are still trying to figure out the best way to handle fastq

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Noam Teyssier @noamteyssier.bsky.social · 09/01/2026

To be one with the borrow checker one must first be willing to let go

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Noam Teyssier @noamteyssier.bsky.social · 12/12/2025

We can make as many pipes as we have threads, each with a fixed record range and with a specified segment (R1 / R2). Then we can connect to each pipe on a reader and treat it as a normal FASTX file. What's great about this is we can process *either* sequentially or in parallel *without* deadlocks!

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Noam Teyssier @noamteyssier.bsky.social · 12/12/2025

This was a fun engineering problem but ultimately was not very difficult because of the way BINSEQ is designed in the first place! Named pipes can be a headache because it requires coordination between readers and writers but because BINSEQ is random access the implementation is straightforward.

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Noam Teyssier @noamteyssier.bsky.social · 12/12/2025

New feature to bqtools v0.4.14 that I'm stoked on! One of the limiting factors to adopting BINSEQ is that it's new and not widely supported by existing tools. `bqtools pipe` addresses this by transparently creating FASTX named-pipes which can be processed normally by existing tools.

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 10/12/2025

If you ever need to fuzzy search some DNA, sassy is your tool. Please spread the word; I think many people just outside my own circle could benefit from this :) cc @rickbitloo.bsky.social github.com/RagnarGrootK...

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Noam Teyssier @noamteyssier.bsky.social · 09/12/2025

Some optimization on VBQ with the latest binseq update, especially in lossless mode. Some ways to trim the fat: 1. Reuse zstd decoders for each thread. I was creating a decoder for each vbq block which incurred redundant allocations 2. Zero-copy parsing of blocks, referencing similar to paraseq

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Noam Teyssier @noamteyssier.bsky.social · 19/11/2025

ARM64 linux I think is pretty common on cloud computing environments. Might be worth to build for it also

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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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Noam Teyssier @noamteyssier.bsky.social · 18/11/2025

Built with uv so you don't have to worry about the dependencies or environments. Simple as: ``` uv tool install anntools-bio anntools --help ```

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Noam Teyssier @noamteyssier.bsky.social · 18/11/2025

I work with large collections of AnnDatas for single-cell work and got tired of opening notebooks for simple operations. Built a CLI tool to handle some common stuff directly from the terminal. Quick ops: downsample, concat, pseudobulk, QC, metadata export, etc. github.com/noamteyssier...

github.com

GitHub - noamteyssier/anntools: a cli-driven anndata toolkit

a cli-driven anndata toolkit. Contribute to noamteyssier/anntools development by creating an account on GitHub.

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

Side note: sandbox.bio is so cool. Setting up an environment where you can learn and play around with these tools in the browser is no simple feat and I think it's an excellent educational resource for the bioinformatics community. I'm very happy and proud to contribute to it!

sandbox.bio

sandbox.bio - Interactive bioinformatics tutorials

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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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Noam Teyssier @noamteyssier.bsky.social · 07/11/2025

The pattern counting is something I'm especially stoked about. I was actually very surprised to see that this feature isn't more common on grep-like tools (outside of bioinformatics as well). I've had this problem for years and I end up writing bespoke tools that do some variation of it.

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Noam Teyssier @noamteyssier.bsky.social · 07/11/2025

New bqtools release with some nice new features! 1. Support for fuzzy matching using sassy 2. Multi-Pattern counting (like `grep -c` but the count is for each individual pattern provided) 3. Pattern files (providing large lists of patterns as either regex or literals) github.com/ArcInstitute...

github.com

Release bqtools-0.4.8 · ArcInstitute/bqtools

What's Changed 116 support fuzzy grep with sassy by @noamteyssier in #118 119 gate fuzzy matching behind feature flag by @noamteyssier in #120 58 implement a pattern count feature by @noamteyssier...

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Noam Teyssier @noamteyssier.bsky.social · 29/10/2025

And stay on the look out the next couple weeks (hopefully) for the release of an even bigger project built with binseq!

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Noam Teyssier @noamteyssier.bsky.social · 29/10/2025

I've updated the BINSEQ manuscript to stay up to date with changes since I originally put it out at the beginning of the year Some notable changes: 1. Support for ambiguous bases with 4bit encoding 2. Support for sequence headers 3. Improved API www.biorxiv.org/content/10.1...

biorxiv.org

BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences

Modern genomics produces billions of sequencing records per run, which are typically stored as gzip-compressed FASTQ files. While this format is widely used, it is not optimal for high-throughput proc...

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Noam Teyssier @noamteyssier.bsky.social · 28/10/2025

Was just about to submit a revision for a paper and realized that I wouldn't be able to submit my source for the text because it was written with typst. Such a bummer - moving this over to tex now but damn what a waste of time! typst is just so much nicer to work with.

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Rick Beeloo @rickbitloo.bsky.social · 23/10/2025

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

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Martin Kampmann @kampmann.bsky.social · 22/10/2025

Thank you Alzforum for featuring our new preprint identifying regulators of disease states of #microglia. Project led by Amanda McQuade, computation by Reet Mishra, collaboration with the Nunez and De Jager labs. Alzforum www.alzforum.org/news/researc... Preprint www.biorxiv.org/content/10.1...

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Noam Teyssier @noamteyssier.bsky.social · 23/10/2025

Had an old tool called `hist` to run `sort | uniq -c` years ago but thought up a high-perf impl for it today. Tried it out and found a 25x throughput over the coreutils version. Big takeaway - arena allocators, hashmaps, and serde work super well together. github.com/noamteyssier...

github.com

GitHub - noamteyssier/hist-rs: An efficient unique-line counter (25x over `sort | uniq -c`)

An efficient unique-line counter (25x over `sort | uniq -c`) - noamteyssier/hist-rs

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Noam Teyssier @noamteyssier.bsky.social · 18/09/2025

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

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Noam Teyssier @noamteyssier.bsky.social · 17/09/2025

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

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Noam Teyssier @noamteyssier.bsky.social · 15/09/2025

bsky.app/profile/noam... Here was a benchmark I ran a while back comparing twobit and binseq on a single-thread

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Noam Teyssier @noamteyssier.bsky.social · 15/09/2025

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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Noam Teyssier @noamteyssier.bsky.social · 04/09/2025

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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Antoine Limasset @npmalfoy.bsky.social · 02/07/2025

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

biorxiv.org

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...

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