CHOPCHOP (version 3) is a web tool for selecting target sites for CRISPR/Cas9, CRISPR/Cpf1, CRISPR/Cas13 or NICKASE/TALEN-directed mutagenesis.

CHOPCHOP can be run with as few as three basic input options, or with additional advanced parameters. The basic input comprises:

  1. a gene name, genomic coordinates or a pasted sequence (including RefSeq and ENSEMBL gene IDs),
  2. a growing list of organisms,
  3. the choice between CRISPR/Cas9, CRISPR/Cas9 Nickase, CRISPR/Cpf1 or TALEN mode.

The advanced options provide the user with more flexibility when choosing target sites.If you would like to run CHOPCHOP locally, you can download the command-line version of the tool here: https://bitbucket.org/valenlab/chopchop/src/master/

If you use our tool please cite at least the latest paper:

Labun, K., Montague, T. G., Krause, M., Torres Cleuren, Y. N., Tjeldnes, H., & Valen, E. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Research (2019).

and if you can:

Labun, K., Montague, T. G., Gagnon, J. A., Thyme, S. B. & Valen, E. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res. 44, W272–6 (2016).


Montague, T. G., Cruz, J. M., Gagnon, J. A., Church, G. M. & Valen, E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 42, W401–7 (2014).

This work was supported by a National Defense Science and Engineering Graduate (NDSEG) Fellowship; the American Cancer Society; the Human Frontier Science Program and the National Human Genome Research Institute (NHGRI) Center for Excellence in Genomics Science.

CHOPCHOP is for non-profit and academic use only. All commercial rights are reserved.