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CrispyCrunch

Get Started

• Read the how to guide
• Create an account
• Design a new experiment
• Start a new analysis
• View your current experiments and analyses

Introduction

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.

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.

Key Features

The advantages of using CrispyCrunch over the underlying tools are:

• Design multiple CRISPR edits as unit and analyze them as a unit. Save time and avoid mistakes by not doing your own record keeping.
• Automatic quality control of CRISPR edits. Just point CrispyCrunch to the FastQ output files of your DNA sequencer.
• Benefit from sophisticated HDR design rules which consider cut-to-insert distance, re-cutting, synonymous mutations, optimal primer length, intron/exon junctions, UTR boundaries and more.
• Pre-filled order forms for reagent vendors.

Related works

• Crispor
• Crispresso
• TagIn
• CrispRVariants
• AmpliCan

Acknowledgements

• Aaron McGeever
• Ben Southgate
• David Dynerman
• Giana Cirolia
• Jason Li
• Joe Hiatt
• Kendell Clement
• Luca Pinello
• Manuel Leonetti
• Martin Kampmann
• Max Haeussler
• Ryan Leenay
• Steve Pollard
• Theo Roth
• Many other people at CZI and the Biohub

Feedback

Questions and comments are welcome! Please email gdingle@chanzuckerberg.com.