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CRISPResso2 provides accurate and rapid genome editing sequence analysis

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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.

Additional information

Editor’s note: This article has been peer-reviewed.

References

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    Akcakaya, P. et al. Nature 561, 416–419 (2018).

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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

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.

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.

Correspondence to Daniel E. Bauer or Luca Pinello.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–15 and Supplementary Notes 1–4

  2. Supplementary Software

Source Data

  1. Source Data, Fig. 1

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Further reading

Fig. 1: Novel features of CRISPResso2.