circlehunter

circlehunter is a pipeline for identifying complex ecDNA using ATAC-Seq data.

Pipeline Overview

Dependencies

All dependencies can be installed using mamba

# install mamba in base environment
conda install -n base -c conda-forge mamba
# create new environment according to environment.yml
mamba env create -f environment.yml
# active the new environment
conda activate circlehunter

Run the Pipeline

circlehunter use a yaml format config file to figure out all samples and their output, to run the analysis processes, a config file is needed. A config template is provided.

# make a directory for analysis
mkdir workspace
cd workspace
# copy and edit the config file
cp ../config-template.yaml config.yaml

modify the configuration file according to the template to fit your requirements, then run the pipeline by

snakemake --snakefile ../Snakefile -j 16 --configfile config.yaml

using -j option to specific maximum number of processes can be used by the pipeline. Check snakemake documents for more options.