CONTENT

1. INSTALL
   a. LINUX SYSTEMS
   b. WINDOWS
   c. MAC
2. BARCODE DESIGNER
3. DEMULTIPLEXER

4. ACKNOWLEDGEMENTS
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1. INSTALL
   The application is available from GitHub:
   https://github.com/pelinakan/UBD.git

   To download it:
   - git clone https://github.com/pelinakan/UBD.git
   
   or:
   
   - download as a tar.gz directly from the gitHub website

   a. LINUX SYSTEMS
   If downloaded archived version, first unpack.
   You can use the binaries provided in /bin/linux.
   You can also build the application yourself:
   Run make:
       make
   
   b. WINDOWS
   Compilation and running is dependent on pThread, available for Windows from http://sources.redhat.com/pthreads-win32/
   Compile .sln using Visual Studio or use binaries available in the package

   c. MAC
   XCode is required for compilation. You can find this from https://developer.apple.com/xcode/
   After installing XCode, just run make:
	   make 
   You can also use the binaries provided in /bin/mac. They may not work due to library dependencies. In that case you will have to build 
   the application manually.

2. BARCODE DESIGNER
   This tool is used for designing a given number of barcodes adhering to a given set of constraints as defined in the "config" file.
   Usage:
   	designBarcodes [options] <output_file_name>
   Options:
	-c [STR]	Configuration file
				Name of file containing the constraints. For an example of how to format this file and the available options, have a look at the "config_example.txt"
	-n [INT]    Number of barcodes to output

3. DEMULTIPLEXER
   This tools is used for recalling the barcodes for a fastq formatted input. 
   Note that the output will not be in the same order as the input, as multiple threads are used to process the input file in parallel. If your data is paired-end, provide the pair file under the -p option to get two output files where the pairing is still kept.
   Usage:   
   	findIndexes [options] <ids.txt> <in.fastq> <out.fastq>
   Options: 
         -m [INT]     allowed mismatches [2]
	 				  Maximum number of mismatches allowed in the barcode for allocation. For a way to determine this variable please see "TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing" (Costea et. al. 2012)
         -k INT     kMer length [1/3*length]
	 				Length of the kMer, also explained in detail in the paper
         -s INT     start position of ID [0]
	 				Start position of the barcode
         -l INT     length of ID [0]
	 				Lenght of the barcode
         -e INT     id positional error [0]
	 				Expected positional error of the barcode. For example, if the barcode should start at base 20 but there is a reason to believe that an indel might occur up to that position, this parameter should be set to 1.
         -p STRING  name of pair file [NULL]
   	 				Name of the pair file, in case of a paired end library. This file will not be checked of barcodes, but it will be outputted in a paired fashion to the input file, so that respective rows are still paired. 

4. ACKNOWLEDGEMENTS
   This work was supported by BILS.