AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

Genome Biol. 2019 Aug 15;20(1):167. doi: 10.1186/s13059-019-1783-3.


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 an open-source software that incorporates single-nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing 1 or multiple haplotypes of a sequenced genome, currently supporting 11 Cas proteins. It also leverages patterns of shared genetic variation to optimize sgRNA design for different human populations. AlleleAnalyzer is available at .

Keywords: CRISPR; Computational biology; Genome editing; Genome surgery; Genomics; sgRNA design.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles*
  • Base Sequence
  • CRISPR-Associated Proteins / metabolism
  • Humans
  • Polymorphism, Genetic
  • RNA, Guide / genetics*
  • Software*


  • CRISPR-Associated Proteins
  • RNA, Guide