CompleteTCR © Kami E. Chiotti, 2015 CompleteTCR is a pipeline that determines the repertoire diversity of paired alpha and beta chains of T cell receptor clones utilizing raw sequence data generated from single paired TCRs as input. ------------------------------------------------------- SYSTEM REQUIREMENTS Java version 1.7 or higher and R version 3.1.0 or higher should be installed on the system. The plyr() package must be installed to R. CompleteTCR consists of three separate scripts: A shell wrapper (completeClone.sh), an R script (completeTCR.R), and a JAR file (completeTCR.jar). All three scripts must be placed within the same directory, and the path to this directory is used as an argument when executing CompleteTCR. USAGE CompleteTCR is a command line application. Full paths are required for all file and tool locations. A COLON-DELIMITED manifest must be provided to CompleteTCR detailing the locations of the input alpha and beta FASTQ files as well as a UNIQUE prefix name. CompleteTCR will create a subdirectory using the prefix name in the designated output directory, and output will be placed in this subdirectory. Manifest format is as follows: Full/Path/To/alpha_fastq:Full/Path/To/beta_fastq:Prefix Execution of CompleteTCR is accomplished on the command line by providing location of the manifest file, the location of the desired output directory, the location of the directory containing the CompleteTCR tool, and the optional parameter for saving all intermediate/temporary files (default is set to F). $ completeClone.sh <Path/To/manifest> <Path/To/output_dir> <Path/To/CompleteClone> <savetmps_TF>