Mutation Reporter: Protein-Level Identification of Single and Compound Mutations in NGS Data

Next-generation sequencing (NGS) has accelerated precision medicine by enabling simultaneous analysis of multiple genes and detection of low-frequency mutations. However, few open-source tools allow non-specialized users to transparently adjust quality parameters during mutation analysis. Mutation Reporter was developed to identify both single and compound amino acid alterations directly from raw fastq files of sequencing originated from RNA or exon sequences. The software provides full parameter control—including alignment e-value, minimum read length, minimum read depth, and minimum variant allele frequency (VAF). The software is freely available under a GNU license on GitHub (\texttt{https://github.com/meidanis-lab/mutation-reporter}).