mitoMaker

mitoMaker is a pipeline script developed to simplify the assembly and automatic annotation of mitochondrial genomes, based on raw NGS reads and an optional target reference.

mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others.

General pipeline:
1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches 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).