14 releases

0.1.32 Feb 13, 2024
0.1.31 May 22, 2023
0.1.29 Mar 13, 2023
0.1.26 Feb 15, 2023
0.1.17 Jul 26, 2022

#64 in Biology

MIT license

1.5K SLoC



MIT licensed actions status codecov

sgcount is a fast and flexible sgRNA counter for CRISPR screens.

This was developed to be a simple yet powerful tool to take raw sequencing files to count tables. This will be the preprocessing step for CRISPRBrain and will eventually be available to perform analysis directly from the browser - but is available here as a standalone tool for those who would prefer local analysis.


sgcount was designed to be a single, easy, and fast interface for researchers who just want to get the results of their CRISPR screen.

To learn more about the features of this tool over existing methods check out the about page.


No wasted time fiddling with conda environments - sgcount is written in rust and is backed by its powerful package manager cargo.

cargo install sgcount

One line installation can be found in the install instructions.


If you're ready to go an run your first screen check out the usage.

sgcount -l <library> -i <sample>

Running differential expression and gene aggregation

Once you have your counts - check out my tool crispr_screen to perform the differential expression and gene-level aggregation.

External Links


~213K SLoC