Box 1.
Application Configuration File for the CAP3 Program
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The first line defines the name of the script used to execute CAP3. The input data and output data are described in the “Main” section. The input is a FASTA file containing the sequences. The program can product two outputs: The first is the sequence assembly (results of CAP3 are converted into fasta format by the launcher script) and the second is the standard output of the program. All command line parameters are optional and are given in an “Options” section. In the configuration file it is possible to specify, for example, default values and the value range.
