CRISPR Comparison ToolKit (CCTK)

Tools to identify and compare CRISPR arrays.

Now published at the CRISPR Journal (https://doi.org/10.1089/crispr.2022.0080)

What is it?

CCTK is a collection of tools written in Python3 that are focused on the comparison of CRISPR arrays that share spacers with one another. CCTK includes two main tools: CRISPRdiff and CRISPRtree which can be used to visualize and analyze the relationships between CRISPR arrays. In addition, CCTK includes two scripts to identify CRISPR arrays genome assemblies and a script to generate a network representation of array relationships. The flow of data between CCTK tools is shown below.

CCTK tools:

1. cctk blast and cctk minced Identify CRISPR arrays in assemblies using a method based on MinCED or BLAST.
2. cctk network Represent spacers shared between arrays as a network.
3. cctk crisprdiff Visualize alignment of homologous arrays.
4. cctk crisprtree Infer maximum parsimony tree explaining array relationships.
5. cctk constrain Assess whether CRISPR array relationships support phylogenetic relationships inferred based on other data (e.g. MLST)
6. cctk spacerblast Identify targets of CRISPR spacers in a BLAST database: assess whole length of imperfect spacer-protospacer matches and check for presence of protospacer adjacent motif (PAM).

Documentation and tutorials

Documentation can be found at Read the docs

Installation

CCTK is a collection of scripts that designed to be run from the command line. Installation is as simple as downloading this repository to your computer and running the scripts in the terminal.

Conda - recommended

CCTK has a number of dependencies to function. These are listed in the Dependencies section below.

Conda can be used to install CCTK and all of its dependencies easily.

The latest version of CCTK can be installed from Anaconda using:

conda install -c bioconda cctk

Git clone

To download this repository using git:

git clone https://github.com/Alan-Collins/CRISPR_comparison_toolkit.git

Dependencies

N.B. some dependencies are only required for certain tools. If you are only using CRISPRtree and CRISPRdiff then you only need python3 with matplotlib and dendropy.

• python3 (Tested with Python >= 3.8)

  • Matplotlib
  • DendroPy
  • NumPy

• MinCED

• BLAST+ (tested with BLAST 2.9.0)