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, currently supporting eleven Cas proteins.  It also leverages patterns of shared genetic variation to optimize sgRNA design for different human populations. AlleleAnalyzer is available at https://github.com/keoughkath/AlleleAnalyzer.

Please see readme and manuscript. 

Please see readme and manuscript.