QualityEncoding

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Sets the quality encoding for the alignment or other NGS module being used.

Options include:

Automatic -- automatically detect quality encoding as either Illumina or Sanger
Sanger -- specifies the file as using Sanger quality encoding.
Illumina -- specifies the file as using Illumina quality encoding

See http://en.wikipedia.org/wiki/Fastq#Quality for more information on quality encoding.