MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

MOTIVATION: Exome capture kits have capture efficiencies that range from 40 to 60%. A significant amount of off-target reads are from the mitochondrial genome. These unintentionally sequenced mitochondrial reads provide unique opportunities to study the mitochondria genome. RESULTS: MitoSeek is an open-source software tool that can reliably and easily extract mitochondrial genome information from exome and whole genome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers and detects heteroplasmy, somatic mutation and structural variants of the mitochondrial genome. MitoSeek can be set up to run in parallel or serial on large exome sequencing datasets. AVAILABILITY: https://github.com/riverlee/MitoSeek