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The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome. AlleleAnalyzer is open-source software that incorporates single nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing one or multiple haplotypes of a sequenced genome from any species, currently supporting eleven Cas proteins. It also leverages patterns of shared genetic variation to optimize sgRNA design for different populations. AlleleAnalyzer is available at

Note: If you use this tool and find any issues or anything that is difficult to interpret, please send a message to this Github or to kathleen.keough at

If you use this tool, please cite our paper in Genome Biology.

Table of Contents

  1. Getting started
  1. Tool descriptions
  1. Tutorials

Useful links

PAM sites in UCSC Genome Browser, hg19

PAM sites in UCSC Genome Browser, hg38

UCSC chromosome fastas, hg19.

UCSC chromosome fastas, hg38.