Signup Login


Get Started


CrispyCrunch is a tool for defining batches of CRISPR edits and analyzing their basic effects. An edit can be either a plain CRISPR/Cas9 cut––a "knock-out"––or a cut plus insertion through HDR––a "knock-in". It was initially built for the CZ Biohub project by Manuel Leonetti to tag all 22,000 protein coding genes in the human genome with GFP.

Example batch CRISPR+HDR experiment from CrispyCrunch

CrispyCrunch uses the popular tool Crispor for finding potential guide sequences––sgRNAs––and for designing primers for PCR amplification. (Crispor in turn uses the ubiquitous primer3 for primer design.) Click here to see an example set of guide sequences from Crispor.

For analysis, CrispyCrunch uses another popular tool, Crispresso. The analysis quantifies the efficiency of knock-in or knock-out edits by repair outcome––NHEJ or HDR. Click here to see an example analysis report from Crispresso.

Guide sequences from Crispor
Edit efficiency from Crispresso

Key Features

The advantages of using CrispyCrunch over the underlying tools are:

Related works



Questions and comments are welcome! Please email