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# A script for running Mosaik Assembler pipeline
# and calling SNPs and short indels using GigaBayes
# chromosome by chromosome for SOLiD mate pairs
# Author: Marcin.Kierczak@hgen.slu.se
# Written: 18.05.2010
# -------------------------------------------------
# Modified and expanded, now using Mosaik suite 1.1.0021
# with Freebayes 0.8.5 (also bamtools and bamaddrg)
# Bash based, autorun, user interface, utilizing
# multiple threads
# Co-author: Andreas.E.Lundberg@gmail.com
# GitHub repo: git://github.com/Papegoja/NGSassembly.git
# Date: 13.07.2011
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Program aligns one chromosome at a time after Build and BuildCS.
Generates individual chromosome directory in results directory. 

First set up working directories and pipeline variables. 
Alignment is done in linear processing fashion using multiple cores. 

All other steps are run IN PARALLEL utilizing user selectable number of threads. 
Build -> BuildCS -> JumpDB -> Align -> RemoveDuplicates -> Sort -> Assemble -> Text -> freebayes

This analysis pipeline requires a lot of disk space. 
Make sure paths are set correctly as script will replace existing results directory. 
All programs need to reside in same directory. 
The reads files are processed from reads directory.