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This project forked from pelinakan/ubd
FinalVersions
CONTENT 1. INSTALL a. LINUX SYSTEMS b. WINDOWS c. MAC 2. BARCODE DESIGNER 3. DEMULTIPLEXER 4. ACKNOWLEDGEMENTS ----------------------------------------------------------- ----------------------------------------------------------- 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.
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