Digenome-sequencing

Genome-wide profiling of off-target effects.


Digenome-seq

Digenome-seq is an in vitro nuclease-digested whole-genome sequencing to profile genome-wide nuclease off-target effects in cells. This in vitro digest yields sequence reads with the same 5' ends at cleavage sites that can be computationally identified by Digenome program.


Citation info: Kim D. et al. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nature Methods 12, 237-243 (2015).


You can download a standalone program for digenome-seq here.



Edit distance calculator
These scripts may contain two parts for calculating edit distance. At first, from.fast.get_29bp.for.revcomp.py should be run to get 29-length DNA base pairs from given chromosome numbers and positions in your reference genome (e.g. hg19, hg38). Next, edit.step.bulge.weight.py will calculate 'edit-distance' between obtained 29-length DNA base pair and RGEN on-target sequence. Second script also gives the edit distance steps which can identify 'addition', 'deletion' and 'subtitution'. Finally, the number of 'deletion' step will be added to edit distance score to assign 'bulge' weight to edit-distance.
Requirement: python-levenshtein(https://pypi.python.org/pypi/python-Levenshtein/)

You can download a standalone program for edit distance calculator here(zip included).



Off-target score calculator

After analyzing 964 sites cleaved in vitro by different 11 sgRNAs and measuring indel frequencies at hundreds of off-target sites in cells, we propose an off-target scoring system of each target site for minimizing CRISPR-Cas9 off-target effects in the human genome. Please note that this off-target score is available for human genome with SpCas9 nucleases.


Citation info: Kim D. et al. Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq. Genome Research doi:10.1101/gr.199588.115 (2016).



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