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

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

Author information

1
Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, CA, USA.
2
Gladstone Institutes, San Francisco, CA, USA.
3
Bioinformatics Graduate Program, University of California, San Francisco, CA, USA.
4
Gladstone Institutes, San Francisco, CA, USA. bconklin@gladstone.ucsf.edu.
5
Departments of Biostatistics, Medicine, Ophthalmology and Pharmacology, University of California, San Francisco, CA, USA. bconklin@gladstone.ucsf.edu.
6
Gladstone Institutes, San Francisco, CA, USA. katherine.pollard@gladstone.ucsf.edu.
7
Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, CA, USA. katherine.pollard@gladstone.ucsf.edu.
8
Chan Zuckerberg Biohub, San Francisco, California, USA. katherine.pollard@gladstone.ucsf.edu.

Abstract

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 https://github.com/keoughkath/AlleleAnalyzer .

KEYWORDS:

CRISPR; Computational biology; Genome editing; Genome surgery; Genomics; sgRNA design

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