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Motivation: The increasing availability of mitochondria-targeted and off-targeted sequencing data in Whole Exome and Genome Sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencingdoi:10.1093/bioinformatics/btu483 pmid:25028726 pmcid:PMC4201154 fatcat:zaukpoou6rekpd3yjrlmmhvfm4