CROPSR: An Automated Platform for Complex Genome-Wide CRISPR gRNA Design and Validation
CABBI Theme: Feedstock Production
Keywords: Genomics, Software
Müller Paul, H., Istanto, D.D., Heldenbrand, J., Hudson, M.E. Nov. 13, 2021. “CROPSR: An Automated Platform for Complex Genome-Wide CRISPR gRNA Design and Validation.” GitHub Repository, https://github.com/cabbi-bio/cropsr.
Functional block diagram of CROPSR modules. (a) The different input data files (FASTA, GFF, Phytozome annotation file) are imported and processed by multiple modular programs within the CROPSR suite. The genome sequence is submitted to the gRNA design program (shown in detail in b), and the output is placed in a MongoDB database (or optionally a CSV file). The GFF file, and Phytozome annotation file when applicable, are processed by a separate program, and then each entry in the database is updated with functional annotation to be used for search queries. Unique primer pairs are designed for each gRNA database entry. (b) The gRNA module takes data from the file manager module (which parses a FASTA input sequence file), and generates a list of location pairs (5 0 − 3 0 ) for every PAM site match. The sequence, strand, start and end positions and CRISPR system for each guide are stored, and a score representing expected performance of each potential gRNA is calculated utilizing one of the available algorithms. Final data for each guide is then added to the database to be associated with functional annotation and PCR primers for validation.
CROPSR is a python tool designed for genome-wide gRNA design and evaluation for CRISPR experiments, with special focus on complex genomes such as those found in energy-producing crops. CROPSR is a product of the DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI).
Paul, H.M., Istanto, D.D., Heldenbrand, J., Hudson, M.E. Feb. 16, 2022. “CROPSR: An Automated Platform for Complex Genome-Wide CRISPR gRNA Design and Validation.” BMC Bioinformatics 23: 74. DOI: 10.1186/s12859-022-04593-2.