May 2, 2025 at 12:56 AM
Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs
github.com/arcInstitute...
github.com/arcInstitute...
GitHub - ArcInstitute/xsra: An efficient CLI to extract sequences from the SRA
An efficient CLI to extract sequences from the SRA - ArcInstitute/xsra
github.com
April 29, 2025 at 9:03 PM
Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs
github.com/arcInstitute...
github.com/arcInstitute...
So cool!!! I really want to try this package. Just what I was looking for! 🧬🖥️ github.com/ArcInstitute...
GitHub - ArcInstitute/ScreenPro2: Flexible analysis of high-content CRISPR screening
Flexible analysis of high-content CRISPR screening - ArcInstitute/ScreenPro2
github.com
December 2, 2024 at 9:32 PM
So cool!!! I really want to try this package. Just what I was looking for! 🧬🖥️ github.com/ArcInstitute...
Paper: arcinstitute.org/manuscripts/...
Blog: arcinstitute.org/news/blog/evo2
GitHub: github.com/ArcInstitute...
Blog: arcinstitute.org/news/blog/evo2
GitHub: github.com/ArcInstitute...
February 19, 2025 at 4:42 PM
scBaseCount
SRA-based
SRAgent #AIAgent-curated
scRecounter gene annotation
Largest scRNAseq database so far 230M cells 72 tissues🤠
10x chemistry only (for now)
#OpenScience #ArcVirtualCellAtlas
github.com/ArcInstitute...
bioRxiv 2025
www.biorxiv.org/content/10.1...
SRA-based
SRAgent #AIAgent-curated
scRecounter gene annotation
Largest scRNAseq database so far 230M cells 72 tissues🤠
10x chemistry only (for now)
#OpenScience #ArcVirtualCellAtlas
github.com/ArcInstitute...
bioRxiv 2025
www.biorxiv.org/content/10.1...
June 27, 2025 at 7:08 PM
scBaseCount
SRA-based
SRAgent #AIAgent-curated
scRecounter gene annotation
Largest scRNAseq database so far 230M cells 72 tissues🤠
10x chemistry only (for now)
#OpenScience #ArcVirtualCellAtlas
github.com/ArcInstitute...
bioRxiv 2025
www.biorxiv.org/content/10.1...
SRA-based
SRAgent #AIAgent-curated
scRecounter gene annotation
Largest scRNAseq database so far 230M cells 72 tissues🤠
10x chemistry only (for now)
#OpenScience #ArcVirtualCellAtlas
github.com/ArcInstitute...
bioRxiv 2025
www.biorxiv.org/content/10.1...
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...
Obligatory BINSEQ mention here - keep a lookout the next couple weeks for an update!
github.com/arcInstitute...
GitHub - ArcInstitute/binseq: A high efficiency binary format for sequencing data
A high efficiency binary format for sequencing data - ArcInstitute/binseq
github.com
January 9, 2026 at 7:06 PM
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...
Obligatory BINSEQ mention here - keep a lookout the next couple weeks for an update!
github.com/arcInstitute...
BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/arcinstitute...
April 18, 2025 at 8:01 PM
BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/arcinstitute...
I've also added some nice functionality to bqtools including a very useful colored grep!
github.com/arcinstitute...
github.com/arcinstitute...
GitHub - ArcInstitute/bqtools: A command line utilty for working with BINSEQ files
A command line utilty for working with BINSEQ files - ArcInstitute/bqtools
github.com
October 29, 2025 at 8:41 PM
I've also added some nice functionality to bqtools including a very useful colored grep!
github.com/arcinstitute...
github.com/arcinstitute...
Today is my first day as Writer-in-Residence at @arcinstitute
I'll be writing about the Virtual Cell, genome editing + much more.
Grateful for the invitation to spend my summer here and learn more about AI+Bio!
I'll be writing about the Virtual Cell, genome editing + much more.
Grateful for the invitation to spend my summer here and learn more about AI+Bio!
June 9, 2025 at 9:35 PM
Today is my first day as Writer-in-Residence at @arcinstitute
I'll be writing about the Virtual Cell, genome editing + much more.
Grateful for the invitation to spend my summer here and learn more about AI+Bio!
I'll be writing about the Virtual Cell, genome editing + much more.
Grateful for the invitation to spend my summer here and learn more about AI+Bio!
Preprint: Genome modeling and design across all domains of life with Evo 2 🧬🖥️🧪 https://arcinstitute.org/manuscripts/Evo2
Source (Apache) https://github.com/arcinstitute/evo2
Source (Apache) https://github.com/arcinstitute/evo2
February 19, 2025 at 4:19 PM
Preprint: Genome modeling and design across all domains of life with Evo 2 🧬🖥️🧪 https://arcinstitute.org/manuscripts/Evo2
Source (Apache) https://github.com/arcinstitute/evo2
Source (Apache) https://github.com/arcinstitute/evo2
xsra is a CLI utility, but makes use of the ncbi-vdb C-library through FFI bindings. We separated the library from the command-line utility so that others could make use of the FFI bindings as well:
github.com/arcInstitute...
github.com/arcInstitute...
GitHub - ArcInstitute/ncbi-vdb-sys: Rust bindings to NCBI-VDB to interact with SRA files programmatically
Rust bindings to NCBI-VDB to interact with SRA files programmatically - ArcInstitute/ncbi-vdb-sys
github.com
April 29, 2025 at 9:03 PM
xsra is a CLI utility, but makes use of the ncbi-vdb C-library through FFI bindings. We separated the library from the command-line utility so that others could make use of the FFI bindings as well:
github.com/arcInstitute...
github.com/arcInstitute...
🆕 On Twitter, @kcoleman has started following @arcinstitute
+ https://x.com/kcoleman
+ https://x.com/arcinstitute
+ https://x.com/kcoleman
+ https://x.com/arcinstitute
September 26, 2025 at 7:07 PM
🆕 On Twitter, @kcoleman has started following @arcinstitute
+ https://x.com/kcoleman
+ https://x.com/arcinstitute
+ https://x.com/kcoleman
+ https://x.com/arcinstitute
#FreeFeatured #Perspective from @li_lingyin at @arcinstitute @Stanford_ChEMH : Stimulating STING for cancer therapy: Taking the extracellular route http://dlvr.it/T71Z5n
May 17, 2024 at 1:01 PM
#FreeFeatured #Perspective from @li_lingyin at @arcinstitute @Stanford_ChEMH : Stimulating STING for cancer therapy: Taking the extracellular route http://dlvr.it/T71Z5n
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...
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/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...
github.com
November 7, 2025 at 1:12 AM
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...
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...
Here's another link to bqtools - our CLI for encoding, decoding, searching, and generally manipulating *.bq and *.vbq
github.com/arcInstitute...
github.com/arcInstitute...
GitHub - ArcInstitute/bqtools: A command line utilty for working with BINSEQ files
A command line utilty for working with BINSEQ files - ArcInstitute/bqtools
github.com
April 21, 2025 at 3:25 PM
Here's another link to bqtools - our CLI for encoding, decoding, searching, and generally manipulating *.bq and *.vbq
github.com/arcInstitute...
github.com/arcInstitute...
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/ArcInstitute...
GitHub - ArcInstitute/binseq: A high efficiency binary format for sequencing data
A high efficiency binary format for sequencing data - ArcInstitute/binseq
github.com
January 22, 2026 at 5:23 PM
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/ArcInstitute...
MULTI-evolve is now available as an open-source design tool, no ML expertise required. And because the framework is modular, it improves alongside the field.
Explore the tool: github.com/ArcInstitute...
Demo: www.youtube.com/watch?v=E3tx...
Explore the tool: github.com/ArcInstitute...
Demo: www.youtube.com/watch?v=E3tx...
How to use MULTI-Evolve to design proteins with machine learning
YouTube video by Arc Institute
www.youtube.com
February 19, 2026 at 7:51 PM
MULTI-evolve is now available as an open-source design tool, no ML expertise required. And because the framework is modular, it improves alongside the field.
Explore the tool: github.com/ArcInstitute...
Demo: www.youtube.com/watch?v=E3tx...
Explore the tool: github.com/ArcInstitute...
Demo: www.youtube.com/watch?v=E3tx...
The Goodarzi Lab is hiring a joint postdoctoral fellow. See Arc open roles: job-boards.greenhouse.io/arcinstitute...
March 12, 2026 at 6:19 PM
The Goodarzi Lab is hiring a joint postdoctoral fellow. See Arc open roles: job-boards.greenhouse.io/arcinstitute...
Premier succès à faire créer à une IA (générative mais spécialisée Evo2 de ArcInstitute) un virus (biologique) nouveau.
www.nytimes.com/2026/08/06/s...
www.nytimes.com/2026/08/06/s...
This A.I. Just Created Viruses Not Found in Nature
Scientists trained artificial intelligence on libraries of DNA and then asked the model to create recipes for viral genomes. Sixteen of them were viable, yielding new viruses.
www.nytimes.com
August 7, 2026 at 5:19 AM
Premier succès à faire créer à une IA (générative mais spécialisée Evo2 de ArcInstitute) un virus (biologique) nouveau.
www.nytimes.com/2026/08/06/s...
www.nytimes.com/2026/08/06/s...
So this is what the opinion/perspective piece would be about --- general principles for the design and proposal of specific formats. I think for many cases, generic libraries / formats could serve well and for others, bespoke formats like binseq may fit well github.com/ArcInstitute...
GitHub - ArcInstitute/binseq: A high efficiency binary format for sequencing data
A high efficiency binary format for sequencing data - ArcInstitute/binseq
github.com
August 5, 2025 at 5:01 PM
So this is what the opinion/perspective piece would be about --- general principles for the design and proposal of specific formats. I think for many cases, generic libraries / formats could serve well and for others, bespoke formats like binseq may fit well github.com/ArcInstitute...
Vevo therapeutics released their 100M perturbed single cell atlas!
- git repo: github.com/ArcInstitute...
- press release: www.prnewswire.com/news-release...
- git repo: github.com/ArcInstitute...
- press release: www.prnewswire.com/news-release...
Vevo Therapeutics Open Sources Tahoe-100M, the World's Largest Single-Cell Dataset, as the Inaugural Contribution to Arc Institute's New Virtual Cell Atlas
/PRNewswire/ -- In a landmark move to advance AI-driven biological research, Arc Institute and Vevo Therapeutics announced today that they have partnered on...
www.prnewswire.com
February 26, 2025 at 9:04 AM
Vevo therapeutics released their 100M perturbed single cell atlas!
- git repo: github.com/ArcInstitute...
- press release: www.prnewswire.com/news-release...
- git repo: github.com/ArcInstitute...
- press release: www.prnewswire.com/news-release...
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...
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 - ArcInstitute/cyto: A mapper for single cell sequencing reads with abstract geometries
A mapper for single cell sequencing reads with abstract geometries - ArcInstitute/cyto
github.com
January 22, 2026 at 5:23 PM
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...
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...
We also show how easy it is to integrate BINSEQ and VBINSEQ into existing tools. Here is a CLI which makes use of the minimap2 rust bindings that accepts FASTQ, BINSEQ, and VBINSEQ inputs.
github.com/arcinstitute...
github.com/arcinstitute...
GitHub - ArcInstitute/mmr: A minimap2 implementation with binseq inputs
A minimap2 implementation with binseq inputs. Contribute to ArcInstitute/mmr development by creating an account on GitHub.
github.com
April 15, 2025 at 2:40 PM
We also show how easy it is to integrate BINSEQ and VBINSEQ into existing tools. Here is a CLI which makes use of the minimap2 rust bindings that accepts FASTQ, BINSEQ, and VBINSEQ inputs.
github.com/arcinstitute...
github.com/arcinstitute...
There are definitely uses that would be difficult to impossible with other tools. See github.com/arcinstitute...
August 20, 2026 at 6:43 AM
There are definitely uses that would be difficult to impossible with other tools. See github.com/arcinstitute...
Just grab the latest:
* simpleaf (github.com/COMBINE-lab/...; also available via bioconda)
or
* cyto (github.com/arcinstitute...; preprint here: www.biorxiv.org/content/10.6..., not my work, but the tool seems great and the devs are very solid)
And you're off to the (much faster) races!
2/2
* simpleaf (github.com/COMBINE-lab/...; also available via bioconda)
or
* cyto (github.com/arcinstitute...; preprint here: www.biorxiv.org/content/10.6..., not my work, but the tool seems great and the devs are very solid)
And you're off to the (much faster) races!
2/2
GitHub - COMBINE-lab/simpleaf: A rust framework to make using alevin-fry even simpler
A rust framework to make using alevin-fry even simpler - COMBINE-lab/simpleaf
github.com
May 11, 2026 at 11:31 AM
Just grab the latest:
* simpleaf (github.com/COMBINE-lab/...; also available via bioconda)
or
* cyto (github.com/arcinstitute...; preprint here: www.biorxiv.org/content/10.6..., not my work, but the tool seems great and the devs are very solid)
And you're off to the (much faster) races!
2/2
* simpleaf (github.com/COMBINE-lab/...; also available via bioconda)
or
* cyto (github.com/arcinstitute...; preprint here: www.biorxiv.org/content/10.6..., not my work, but the tool seems great and the devs are very solid)
And you're off to the (much faster) races!
2/2