First step
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Run Red without arguments. It will display a usage message and examples.
      
Running Red
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Memory: Red requires about 6 G of memory if the genome of interest is large, e.g. the human genome or the value of the parameter ``-len`` is 15. When the word length specified with the parameter ``-len`` is 16, about 18 G of memory are required.

Input: Red can process FASTA files ending with the ``.fa`` extension. These files are in two directories. Files in the directory provided with the parameter ``-gnm`` are used to complete the table of the adjusted counts. In addition, these files are scanned for repeats. Files in the directory provided with the parameter ``-dir`` are scanned for repeats; however, they are not used for completing the table. In sum, if the user wishes to scan a genome for repeats, the directory including the FASTA files of this genome should be provided to Red via the ``-gnm`` parameter. Synthetic sequences or sequences of a different species may be placed under a different directory that is provided to Red via the ``-dir`` parameter. 

Output: Red can output the scores of the sequences (``-sco``), the coordinates of the candidate regions (``-cnd``), the coordinates of the final repeats (``-rpt``), the masked sequences (``-msk``), the table of the adjusted counts (``-tbl``), and the hidden Markov model (``-hmo``). The user should use the parameter(s) representing the desired output format(s). For example, the pair ``-rpt directory`` instructs Red to write the genomic locations of the final repeats found in each chromosome of the genome to a new file under the provided directory. Multiple formats can be used simultaneously. Because each output format has its own extension, one directory may be used as the output directory for multiple formats. Sequences under the directories provided to Red via the ``-gnm`` and ``-dir`` parameters must have different names. 

Examples
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The following command runs Red with the defaults and generates the masked sequences.

Red -gnm genome_directory -msk output_directory

The following command runs Red with the defaults and generates the masked sequences and the locations of the repeats found in the whole genome.
	
Red -gnm genome_directory -msk output_directory -rpt output_directory


Processing unassembled genomes
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The parameter ``-min`` should be set to 3 x the average coverage. The user may try to use the parameter ``-len`` with values higher than the default by one or two. It is recommended to divide the short reads into several files.

Note
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The Methods and the Supplementary Methods sections of the paper provide details about how Red operates and the meaning of each parameter.


