Mutation Reporter: fast identification of mutations in NGS files

ABSTRACT Summary 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). Availability and implementation Mutation Reporter is available to users through a free GNU software license and can be accessed on GitHub ( https://github.com/meidanis-lab/mutation-reporter ) and as a Code Ocean capsule ( https://codeocean.com/capsule/0121109/tree ).