bttoxin-pipeline/tools/crispr_cas_analysis

CRISPR-Cas Analysis Module

This module provides tools for detecting and analyzing CRISPR-Cas systems in bacterial genomes using CRISPRCasFinder and MacSyFinder.

Installation & Setup

This directory is a standalone pixi project.

1. Enter the directory:

   cd tools/crispr_cas_analysis
   

2. Install dependencies:

   pixi install
   

3. Install CASFinder Definitions: This step downloads the required CASFinder model definitions.

   pixi run install-casfinder
   

Usage

Environment

To run commands, you can either prepend pixi run or enter the shell:

pixi shell

Running Detection

Use the provided CRISPRCasFinder.pl script to analyze a genome assembly (FASTA format).

Example Command (running from tools/crispr_cas_analysis directory):

# 1. Clean up previous results if they exist
rm -rf tests/test_output
# 先创建输出目录（如果不存在）
mkdir -p ./tests/test_output

# 进入输出目录
cd ./tests/test_output

# 从这里运行命令，调整相关路径
pixi run perl ../../src/CRISPRCasFinder.pl \
-in ../20141126CLLT035_contig341.fna \
-out . \
-so ../../src/sel392v2.so \
-cas -q -log

# # 2. Run detection using relative paths
pixi run perl src/CRISPRCasFinder.pl \
  -in ./tests/20141126CLLT035_contig341.fna \
  -q -cas -log -html -ccvRep \
  -cpuMacSyFinder 20   \
  -cluster 20000 \
  -getSummaryCasfinder \
  -so /home/gzy/Bt_Project/software/sel392v2.so \
  -gffAnnot /home/gzy/Bt_Project/1_sequencing_genome_annotation/20120412LHLT139/20120412LHLT139.gff \
  -proteome /home/gzy/Bt_Project/1_sequencing_genome_annotation/20120412LHLT139/20120412LHLT139.faa
  -out ./tests/test_output \
  -so ./src/sel392v2.so

Output Explanation

The output directory (tests/test_output) will contain several key files:

• CRISPR-Cas_summary.tsv: Summary of detected CRISPR arrays and Cas systems.
• Cas_REPORT.tsv: Detailed report of detected Cas proteins.
• Crisprs_REPORT.tsv: Detailed report of detected CRISPR arrays.
• GFF/: Annotations of the findings.
• Visualization/: HTML visualization of the results.

Directory Structure

• src/: Source code and scripts (CRISPRCasFinder.pl, etc.).
• scripts/: Wrapper scripts for the pipeline.
• tests/: Test data.