Профиль

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!

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

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.

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

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

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!

Efficient sequence analysis with bqtoolsInteractive bqtools tutorial: learn to analyse sequence data efficiently with BINSEQ files using a command-line interface in your browser.sandbox.bio

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...

Release bqtools-0.4.8 · ArcInstitute/bqtoolsWhat'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...github.com

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...

BINSEQ: A Family of High-Performance Binary Formats for Nucleotide SequencesModern 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...www.biorxiv.org

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.

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 - 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-rsgithub.com

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!

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

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