CRISPR Comparison Toolkit (CCTK)
CCTK is a Python toolkit for the identification and comparison of CRISPR arrays. It includes tools to go from assemblies to publication-quality images and is built around simple file formats to allow users to easily fit CCTK tools into existing workflows.
See the Usage section for further information, including Installation instructions.
See the Tutorial page for a detailed worked example with a downloadable test dataset.
CCTK Tools
blast - Find CRISPR arrays in assemblies using BLASTn
minced - Find CRISPR arrays in assemblies using minced
crisprdiff - Produce a CRISPRdiff plot comparing CRISPR arrays
crisprtree - Perform a maximum parsimony analysis on CRISPR arrays
constrain - Predict array relationships constrained by a tree
network - Produce a network representation of spacer sharing among arrays
evolve - Perform in silico evolution of CRISPR arrays
spacerblast - BLAST spacers against a BLASTdb, process output & check for PAMs