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, 18:34, 19 October 2014
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| See [[#Reference Files|Reference Files]] for the required reference file settings. | | See [[#Reference Files|Reference Files]] for the required reference file settings. |
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− | See [[#Sequence Index File|Sequence Index File]] for how to set the index file either via command line options or via configuration. | + | See [[#FASTQ List File|FASTQ List File]] for how to set the index file either via command line options or via configuration. |
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| ==== Turning Off Optional Steps==== | | ==== Turning Off Optional Steps==== |