Program:
MITObim v1.7 (beta)

Comments:
The MITObim procedure (mitochondrial baiting and iterative mapping) represents a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads.

Source:
https://github.com/chrishah/MITObim

Cite:
Hahn, C., Bachmann, L., & Chevreux, B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach. Nucleic Acids Research, 41(13), e129. doi:10.1093/nar/gkt371

Compilation:
MITObim is a Perl script. It does not require compilation/installation. Simply put MITObim.pl at the desired directory and give it executable permissions .