mitoMaker
mitoMaker - a mitochondria assembly and annotation script
... a target mitochondrial genome given.
2-searches for all mitochondrial gene features and circularization.
3-stores the best result found.
4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps.
5-annotates the best assembly, identifying the start and end position of each and every feature.
6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile).