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Restriction Enzyme Predictor Barcode Generator
Demultiplexer Barcode Discovery

Barcode Generator

mandatory parameters:
* -b the number of barcodes needed
* -e the enzyme used for the experiment

optional parameters:
* -ef the enzyme file. This option adds new enzymes.
The file must be tab delimited: First column the enzyme name, second column the cutsites remains (comma separated) (example: enzyme ApeKI and restriction site G^CWGC: “ApeKI \tab CAGC,CTGC”).
* -nb the maximum number of bootstraps that must be executed. (optional, standard 10000). By the start of a new bootstrap a complete new design is made. The best scored design (most random barcodes and best scored bases distribution is kept as result)
* -bt the number of barcode tries. (standard 20) If a random barcode does not fit into the current design try this number of times with a new random barcode before restarting the bootstrap.
* -o the output directory (standard current working directory)
* -us try to find the ultime match: the best barcode combination with the best bases distribution (standard false) true: continue even when the right number of barcodes is found.
* -bf a file with all barcodes that are used as basic set (this file is one of the possible output files)
* -nf a file with all barcodes that may not be used in the design. If this file contains barcodes that are also found in the basic set file, these barcodes will be replaced in the design by new random barcodes.