An article published in BMCBioInformatics presents MitoHiFi: a python pipeline that can assemble mitochondrial genomes from a wide phylogenetic range of taxa from the PacBio high fidelity (HiFi) sequencing reads.
]. These features were not evident in, or accessible through, previous short-read or PCR-and-sequence approaches.
The increase in the rate of generation of reference genomes across biodiversity using accurate long reads offers an opportunity to revisit the evolution of the gene content and structure of mitochondrial genomes. This opportunity requires development of robust pipelines that reliably assemble organellar genomes, correctly report repeat content, resolve heteroplasmy and distinguish true mitochondrial genome sequence from the frequent presence of nuclear genome inserted copies .
As primary input, MitoHiFi takes Pacbio HiFi reads , or contigs assembled from those reads , and a reference mitochondrial genome from a closely-related species along with its annotation in GenBank format. The pipeline includes a script to automatically download closely-related mitochondrial genomes based on the NCBI taxonomy . The defaults are set to download a single reference genome from the same or most-closely related species, but multiple references can be downloaded by setting -n .
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