Welcome!

This is the SUPER quick guide to MOCAT.
After installation you can run MOCAT in either of these ways:


==== runMOCAT.sh ====

> runMOCAT.sh
This is used for running multiple MOCAT commands in a row, 
which is generally what you want. If you want to generate mOTU
and taxonomic profiles, or assemble metagenomes and predict genes?
- USE THIS!



==== MOCAT.pl ====

> MOCAT.pl
This is the actual MOCAT executable, which is invoked by runMOCAT.sh.
Using MOCAT.pl you can run only few steps or run multiple steps on a project.
Advanatage is that you decide exactly which steps to run, but it may be confusing
which steps are needed to be run in order to create taxonomic and mOTU profiles.
So, if you're unsure, use runMOCAT.sh and once you get the hang of using MOCAT
or if you need to re-run a specific step only, use MOCAT.pl



==== Example scripts in /article_dataset folder ====

> GENERATE_MOTU_AND_TAX_PROFILES.sh
This script does the same thing as running 'runMOCAT.sh' and choosing to create
taxonomic and mOTU profiles without removing human contaminants. This is a generic
script you can copy to your project folder and just execute to create these profiles.
(This script is available in the mock_community folder).

> RUN_PIPELINE.sh
These scripts are specific for each dataset and reproduces the results form the MOCAT
paper. You can use the as examples to understand how to run MOCAT on your dataset.

