Please cite the following tools which are part of AmpliconSuite-pipeline in your work, where applicable AmpliconSuite-pipeline & AmpliconClassifier https://www.biorxiv.org/content/10.1101/2024.05.06.592768v1 AmpliconArchitect https://pubmed.ncbi.nlm.nih.gov/30674876/ BWA MEM https://arxiv.org/abs/1303.3997 CNVkit https://pubmed.ncbi.nlm.nih.gov/27100738/ SAMtools https://pubmed.ncbi.nlm.nih.gov/19505943/