:clipboard: Prerequisites

1) This pipeline is written in nextflow. Install nextflow by following the steps at Nextflow Installation Guide

2) The processes run on Docker containers. Install docker engine by following steps at Docker Installation Guide for Ubuntu

:computer: 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 directory> --out_dir <output directory> -profile <docker or conda>

For example:

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

or

nextflow run Katmon --in_dir Samples --out_dir Results -profile conda

You can also view the help documentations by:

nextflow run Katmon --help

:open_file_folder: Results

Output directory will have 8 folders containing results from each step used to test for SARS-CoV-2 variant coinfection. The summary report is in the final folder named 08-Report with the file name as summary-report.html.

Test the pipeline using sample files

To test the pipeline, use the files from Sample Files. Decompress samples.tar.xz by:

tar -xvf samples.tar.xz