Bareback - Barcode Back-Processing for low complexity Illumina libraries
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Bareback is supposed to rename all folders in a specified Illumina Run folder 
so that an arbitrary number of cycles can be shuffled from the start of the 
sequence to the end. This is a necessary step before the raw image files can 
be reanalysed using the GOAT pipeline. Once the GOAT reanalyis is finished,
the shuffled bases need to be moved to the start of the fastQ sequences again.
An easy-to-use file to shuffle bases back to the start will be included in the
download.

Bareback reads in the RunInfo.xml file to extract information about the type 
of run and number of cycles performed. It will then check whether all image 
folders and files that are to be renamed are present. Only when all images 
are found it will ask for the number of cycles to be shuffled. The renaming 
procedure will start after a last safety question.

IMPORTANT: Please ensure that all data is properly backed up before performing 
any file or folder name operations. 
  
The following is a brief description of command line options and arguments to
control the bareback script:   

USAGE: bareback [options] <run_folder>* <cycles_to_be_moved>
   
<run_folder>          The path to the Illumina run folder directory. Typically 
                      something like /01012010_HWUSI-....._GVAAAXX/. This folder 
                      must contain a file called "RunInfo.xml" which is needed 
                      to extract required run data, and a subfolder called Images/ 
		      which holds all the raw image data of the lanes that are to 
		      be bareback processed. Specifying the run folder is mandatory 
		      (*).
  
<cycles_to_be_moved>  The number of cycles which are intended to be shuffled to the 
		      end of the run (only the first run in case of a paired-end run).
		      If this number is not specified when calling the script the 
		      user will be prompted to enter it at a later stage.   


Problems?

If you have any problems using Bareback please report these into our bug reporting 
tool at:

www.bioinformatics.bbsrc.ac.uk/bugzilla/

..or report them directly to felix.krueger@bbsrc.ac.uk