Mitomaker is a pipeline wrapper, result analyzer and automated annotator, written in Python v2.7, that,
with the help of other programs, builds, analyzes, looks for the best build and annotates target genomes
(such as mitochondria and cloroplast). It could be used with other targets, such as specific genes, or
transcriptomes, even though that is not it's primary goal, nor thoroughly tested.
After various attempts to build different mitochondrial genomes in the lab I studied, a general pipeline
started to appear: assemble reads with MIRA or SOAPdenovo-Trans, look for a scaffold/contig that matches a
closely-related species, check it to see if all expected genomic features are present (since mitochondria is
well conserved), check to see if the assembly might have circularized (since it's a circular DNA). If a
feature was missing, or it hasn't circularized, try and assemble again with different assembler parameters
(mainly k-mer). Rinse and repeat until the best build is found and then annotate it.
Doing these steps automatically, in order to increase efficiency, is basically what mitomaker was made for.
All the credit for the developers of the various programs which are used during this pipeline script, such as
SOAPdenovo-Trans, MIRA, MITObim, tRNAScan-SE, and Blast+.
IMPORTANT NOTICES:
Remember to change the folders of your main programs in the config file, if required.
Main subprograms are provided, but should you encounter errors, install them independantly (links are provided in the manual),
and change the folders in the config file.
Read the manual before starting to use this script for information on installing the required programs and libraries.
Test the program by running test.py, whichy is located in the main script's folder.
