RT Journal Article
SR Electronic
T1 multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets
JF Life Science Alliance
JO Life Sci. Alliance
FD Life Science Alliance LLC
SP e202000757
DO 10.26508/lsa.202000757
VO 3
IS 11
A1 Aditya M Bhagwat
A1 Johannes Graumann
A1 Rene Wiegandt
A1 Mette Bentsen
A1 Jordan Welker
A1 Carsten Kuenne
A1 Jens Preussner
A1 Thomas Braun
A1 Mario Looso
YR 2020
UL https://www.life-science-alliance.org/content/3/11/e202000757.abstract
AB Targeting the coding genome to introduce nucleotide deletions/insertions via the CRISPR/Cas9 technology has become a standard procedure. It has quickly spawned a multitude of methods such as prime editing, APEX proximity labeling, or homology directed repair, for which supporting bioinformatics tools are, however, lagging behind. New CRISPR/Cas9 applications often require specific gRNA design functionality, and a generic tool is critically missing. Here, we introduce multicrispr, an R/bioconductor tool, intended to design individual gRNAs and complex gRNA libraries. The package is easy to use; detects, scores, and filters gRNAs on both efficiency and specificity; visualizes and aggregates results per target or CRISPR/Cas9 sequence; and finally returns both genomic ranges and sequences of gRNAs. To be generic, multicrispr defines and implements a genomic arithmetic framework as a basis for facile adaptation to techniques recently introduced such as prime editing or yet to arise. Its performance and design concepts such as target set–specific filtering render multicrispr a tool of choice when dealing with screening-like approaches.