This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Targeted C•G-to-T•A base editing with TALE-cytosine deaminases in plants
BMC Biology Open Access 29 April 2024
-
Improving prime editing with an endogenous small RNA-binding protein
Nature Open Access 03 April 2024
-
Inhibition of 7-dehydrocholesterol reductase prevents hepatic ferroptosis under an active state of sterol synthesis
Nature Communications Open Access 12 March 2024
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Code availability
CRISPResso2 is available online at http://crispresso2.pinellolab.org, where users can run up to four samples simultaneously. The command line version without any limitations and with additional tools is available as a Docker image at https://hub.docker.com/r/pinellolab/crispresso2/ (Supplementary Note 4). The source code is available as Supplementary Software and online at https://github.com/pinellolab/CRISPResso2.
Data availability
Fig. 1a–c shows data available as SRR3305546 (untreated), SRR3305543 (BE1), SRR3305544 (BE2) and SRR3305545 (BE3)2. Figure 1d shows data obtained from the authors of ref. 10.
References
Tsai, S. Q. & Joung, J. K. Nat. Rev. Genet. 17, 300–312 (2016).
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Nature 533, 420–424 (2016).
Komor, A.C. et al. Sci. Adv. 3, eaao4774 (2017).
Kim, Y. B. et al. Nat. Biotechnol. 35, 371–376 (2017).
Akcakaya, P. et al. Nature 561, 416–419 (2018).
Pinello, L. et al. Nat. Biotechnol. 34, 695–697 (2016).
Wang, X. et al. Bioinformatics 33, 3811–3812 (2017).
Park, J., Lim, K., Kim, J.-S. & Bae, S. Bioinformatics 33, 286–288 (2017).
Lindsay, H. et al. Nat. Biotechnol. 34, 701–702 (2016).
Li, P. et al. CRISPR J. 1, 55–64 (2018).
Acknowledgements
D.R.L. is supported by DARPA HR0011-17-2-0049; US NIH RM1 HG009490, R01 EB022376 and R35 GM118062; and the HHMI. J.K.J. is supported by DARPA HR0011-17-2-0042, NIH R35 GM118158 and NIH RM1 HG009490. D.E.B. is supported by the NIDDK (R03DK109232), NHLBI (DP2OD022716, P01HL32262), Burroughs Wellcome Fund, Doris Duke Charitable Foundation and St. Jude Children’s Research Hospital Collaborative Research Consortium. L.P. is supported by NHGRI (R00HG008399), DARPA HR0011-17-2-0042, and the Centers for Excellence in Genomic Science of the National Institutes of Health under award number RM1HG009490 through a New Collaborator Grant subaward.
Author information
Authors and Affiliations
Contributions
K.C. and L.P. conceived the project, led the study and wrote the software. K.C. analyzed experimental data. All authors contributed input on measurement and visualization of genome editing outcomes and provided input on the manuscript.
Corresponding authors
Ethics declarations
Competing interests
At the time of manuscript preparation, J.M.G. was a consultant for Beam Therapeutics, and now is employed by Beam Therapeutics. J.K.J. has financial interests in Beam Therapeutics, Editas Medicine, Endcadia, EpiLogic Therapeutics, Pairwise Plants, Poseida Therapeutics and Transposagen Biopharmaceuticals. J.K.J.’s interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies. J.K.J. is a member of the Board of Directors of the American Society of Gene and Cell Therapy. J.M.G. and J.K.J. are co-inventors on patents and patent applications that describe gene editing technologies. D.R.L. is a consultant and cofounder of Editas Medicine, Pairwise Plants and Beam Therapeutics, companies that use genome editing.
Additional information
Editor’s note: This article has been peer-reviewed.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–15 and Supplementary Notes 1–4
Source Data
Rights and permissions
About this article
Cite this article
Clement, K., Rees, H., Canver, M.C. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol 37, 224–226 (2019). https://doi.org/10.1038/s41587-019-0032-3
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41587-019-0032-3
This article is cited by
-
Decoding the complexity of on-target integration: characterizing DNA insertions at the CRISPR-Cas9 targeted locus using nanopore sequencing
BMC Genomics (2024)
-
Undetectable off-target effects induced by FokI catalytic domain in mouse embryos
Genome Biology (2024)
-
Targeted C•G-to-T•A base editing with TALE-cytosine deaminases in plants
BMC Biology (2024)
-
Improving prime editing with an endogenous small RNA-binding protein
Nature (2024)
-
Efficient prime editing in mouse brain, liver and heart with dual AAVs
Nature Biotechnology (2024)