📋 Prerequisites

1. This pipeline is written in Nextflow.

2. If you want to run through Docker, follow the Docker installation guide for Ubuntu.

🌼How to use Katmon

1. Download this github repository using git clone.

git clone https://github.com/lanadelrea/Katmon

2. Navigate to the directory where Katmon is downloaded. Run the pipeline by indicating the path to the input and output folders. The input directory should contain fasta, fastq, bam, and bam index files. Remove the slash "/" after the input and output directory. You can run the pipeline using docker or conda by indicating the -profile.

nextflow run Katmon --in_dir <input dir> --out_dir <output dir> -profile <docker or conda>

For example:

nextflow run Katmon --in_dir /Samples --out_dir /Results -profile docker

You can also view the help documentations by:

nextflow run Katmon --help

📂 Results

Output directory will have 7 folders containing results from each step used to test for SARS-CoV-2 variant coinfection. The summary report is in the final folder named 07-Report with the file name as summary-report.html.