PT  - JOURNAL ARTICLE
AU  - Bhagwat, Aditya M
AU  - Graumann, Johannes
AU  - Wiegandt, Rene
AU  - Bentsen, Mette
AU  - Welker, Jordan
AU  - Kuenne, Carsten
AU  - Preussner, Jens
AU  - Braun, Thomas
AU  - Looso, Mario
TI  - multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets
AID  - 10.26508/lsa.202000757
DP  - 2020 Nov 01
TA  - Life Science Alliance
PG  - e202000757
VI  - 3
IP  - 11
4099  - http://www.life-science-alliance.org/content/3/11/e202000757.short
4100  - http://www.life-science-alliance.org/content/3/11/e202000757.full
SO  - Life Sci. Alliance2020 Nov 01; 3
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.