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There are common options for most BBMap suite programs and depending on the file extension the input/output format is automatically chosen/set.

Note: For most programs in BBTools, you can add the parameter "config=foo.txt". Every line in "foo.txt" will be added as if it were a command-line parameter, regardless of whitespace, or the length of the file. This may be convenient if you use a certain set of parameters for different set of analyses.

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