mtGrasp: Streamlined reference‐grade mitochondrial genome assembly and standardization to enhance metazoan mitogenome resources

Abstract High‐quality, accessible mitogenome sequences are crucial for comparative genomics, phylogenetic constructions and environmental DNA (eDNA) applications. With advancements in sequencing technologies, genomic sequencing reads are available for a wide variety of species. Although these data sets contain mitochondrial sequences, this information remains largely untapped due to the limited specialized tools for assembling mitogenomes from short‐read libraries. The present study introduces the Mitochondrial Genome Reference‐grade Assembly and Standardization Pipeline (mtGrasp), a streamlined and memory‐efficient pipeline for assembling complete and standardized mitogenomes from short‐read metazoan DNA libraries ( https://github.com/bcgsc/mtGrasp ). We assembled 23 short‐read libraries and found that mtGrasp ran 2–7 times faster and used 3–4 times less memory, on average, compared to the state‐of‐the‐art mitogenome assembly pipelines GetOrganelle and MitoZ. Additionally, mtGrasp successfully assembled mitogenomes of varying completeness across different animal taxa. We illustrate that standardizing existing mitogenome annotations with mtGrasp would improve the accuracy of downstream phylogenetic analysis and demonstrate the utility of mtGrasp in designing robust targeted quantitative polymerase chain reaction‐based eDNA assays using mitogenomes assembled from museum voucher specimens. We expect the reference‐grade mitogenomes generated with freely available mtGrasp to advance the development of robust, high‐quality eDNA tools and aid in a variety of comparative genomic analyses.