Original author: Michelle Spoto Contributing authors: Sierra Mellor, Georgia Doing

Being updated (Summer 2023) with further development to use for selecting PAMless guides.

These updates, found in GuideFinder_Mac_2020_SMM_PAMless, allows for a selection of NGG, NAN, or NNN PAM sites for guide design. There are also some small fixes and streamlining to guide filtering, as well as additional output files. No changes were made to the pre-processing script.

Pan-bacterial, genome-wide guide designer

README: The Guide Finder program is designed to select guides targeting genes in any bacterial species. Draft genome annotations may be used for guide design, but must be pre-processed to format properly prior into input into the Guide Finder program (a pre-processing script is provided). See the Protocols folder for more information on how to run the program. Instructions for the use of both complete and draft genome annotations is provided in this folder. Example exercises for the use of either a complete or draft genome annotation have also been provided (see respective folders). It is highly recommended that users read through these provided protocols and work through the exercises prior to use of either the pre-processing or the Guide Finder scripts.