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, Docker and/or Conda

How to use Katmon

1. Download this github repository using git clone.

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

2. There seems to be a persistent permision denied error when running the pipeline. According to the internet, it's because I wrote the scripts on Windows locally. For the pipeline scripts to work, kindly do chmod -R 777 Katmon before running the pipeline.

3. 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 --indir <input dir> --outdir <output dir> --sequence <illumina OR ont> -profile <docker OR conda>

For example:

nextflow run Katmon --indir /mnt/d/Samples --outdir /mnt/d/Results --sequence illumina -profile docker

Currently available parameters are as follows:

    Required arguments:
                 
        --indir              Input directory containing FASTA, FASTQ, BAM, and BAM index files
        --outdir             Output directory for results
        --sequence           Can be 'illumina' or 'ont'

    Optional arguments:
        --bammix_thresh      Set the bammix threshold for the proportion of the major allele
                                        Default: 0.8
        --primer_scheme      Primer scheme bed file (ex. /primer-schemes/nCoV-2019/V4.1/SARS-CoV-2.scheme.bed)
        -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.