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mitoMaker_1.14.tar.gz 2014-12-06 52.6 MB
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	   mitoMaker 1.0

            `-://///:-`            
        ./oyhysooooosyhys/.        
     `/oys+/-----------/osys:`     
    :yho:-----------------:oyy:    
  `oys:------------+yyhhys+::syo   
  sys-------------shddddddddo-sho  
 /yh----:://+++++ohhdddddhddd:-hh: 
 yso-+syhdhdddhddhddddddhydddo-oys 
 ys/yhdddddddddddddddddddyddd+-/yh 
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  `ohy:------:::::::--------:sy+   
    :yyo:-----------------:oys-    
     `:shyo/-----------/+sho:`     
        ./oyhhyooooosyhso/`        
            `.::///:-.`            


INSTALL:
Open the INSTALL file for installation and working instructions.

DESCRIPTION:
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).

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, which is located in the main script's folder.
Source: README, updated 2014-08-20