This pipeline was initially designed to investigate potential Delta and Omicron co-infections after anomalous sequences were detected during routine genomic surveillance. More recent developments have expanded its capability to identify potential co-infections involving any SARS-CoV-2 variants—including newer variants and cases involving two lineages within the same clade.

Prerequisites

Nextflow and Docker

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.

nextflow run Katmon --in_dir <input dir> --out_dir <output dir>

For example:

nextflow run Katmon --in_dir /mnt/d/Samples --out_dir /mnt/d/Results

Currently available parameters are as follows:

    Required arguments:
                 
        --in_dir             Input directory containing FASTA, FASTQ, BAM, and BAM index files
        --out_dir            Output directory for results
                  
    Optional arguments:
        --bammix_thresh      Set the bammix threshold for the proportion of the major allele
                                        Default: 0.8
        -profile             Can be docker or conda
        -resume              To resume the pipeline
        -w                   The NextFlow work directory 
                             Delete this directory once the process is finished
                                        Default: ${workDir} 

    Use `nextflow run Katmon --help` to view the help message

Results

Output directory will have 8 folders containing results from each step used to test for SARS-CoV-2 variants co-infection. The summary report is in the final folder named 08-Report with file name as summary-report.html. You can view sample results here.