Nanopore Guide Design

Nextflow implementation for generating, filtering, and prioritizing candidate guide RNA sequences for Nanopore sequencing

Requirements

• Nextflow
• conda distribution (Anaconda or Miniconda) https://www.anaconda.com
• BEDtools
• CHOPCHOP (use the README here for installation/configuration)
• CRISPRon scripts (need to create repo for these)

Configuration

Create conda environments

conda env create -f chopchop.yml && conda env create -f crispron.yml

Update nextflow.config

output = "/path/to/output"
chopchop_path = "/path/to/chopchop.py"
bedtools_path = "/path/to/bedtools"
crispron_path = "/path/to/crispron"

Update guide_design.nf

process parallel_chopchop
conda '/path/to/conda/env/chopchop'

process parallel_crispron
conda `/path/to/conda/env/crispron'

Usage

To run Nextflow pipeline from the repository directory:

nextflow run guide_design.nf -output-dir /path/to/output

To test different paramaters (eg. distance) run:

nextflow run guide_design.nf -output-dir /path/to/output --distance 2000