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Digenome-seq web tool for profiling CRISPR specificity

Nature Methods volume 14, pages 548–549 (2017)Cite this article

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To the Editor:

We recently reported Digenome-seq (digested genome sequencing), a method for in vitro identification of potential off-target sites, and we evaluated the specificity of CRISPR–Cas9 (refs. 1,2) and CRISPR–Cpf1 (ref. 3) endonuclease by whole-genome sequencing. Digenome-seq pinpoints the exact location of double-strand break (DSB) sites by recognizing specific patterns of aligned reads. However, the analysis pipeline presented in our previous report required extensive manual interaction and produced several large intermediate files, resulting in a long running time. Here, we present a redesigned analysis tool for Digenome-seq data that runs on web browsers. The core algorithm of the tool is written in C++ and compiled to asm.js (http://asmjs.org/), a preoptimized subset of JavaScript. Users can instantly perform the complete analysis in an ordinary web browser (Supplementary Note 1) with fast execution speed without uploading any data to a server and without local tool installation. In our benchmark, the full analysis for 100 GB of BAM file took 3 h for whole analysis on Intel i5 3570k central processing unit in a single thread.

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Figure 1: Digenome-seq overview.

References

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Acknowledgements

We thank M. Schlesner and R. Eils for helpful discussion. This work was supported by the Institute for Basic Science grant no. IBS-R021-D1 to J.-S.K. and Next Generation BioGreen 21 Program grant no. PJ01119201 and Korea Healthcare technology R&D Project grant no. HI16C1012 to S.B.

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Authors and Affiliations

  1. Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Jeongbin Park & Liam Childs

  2. Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea

    Daesik Kim, Sunghyun Kim, Sang-Tae Kim & Jin-Soo Kim

  3. Department of Chemistry, Hanyang University, Seoul, South Korea

    Gue-Ho Hwang & Sangsu Bae

  4. Department of Chemistry, Seoul National University, Seoul, South Korea

    Jin-Soo Kim

  5. Institute of Nano Science and Technology, Hanyang University, Seoul, South Korea

    Sangsu Bae

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  1. Jeongbin Park
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  2. Liam Childs
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  3. Daesik Kim
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Correspondence to Jin-Soo Kim or Sangsu Bae.

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S.B. and J.P. have filed a patent application based on this work.

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Park, J., Childs, L., Kim, D. et al. Digenome-seq web tool for profiling CRISPR specificity. Nat Methods 14, 548–549 (2017). https://doi.org/10.1038/nmeth.4262

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