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Old 02-19-2014, 02:14 PM   #2
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If the first data set was done a few years ago you would want to check what format the quality values are in. They may be in "illumina" format and would need to be converted to "sanger" quality if you are going to do any combined analysis. (Ref:

Depending on the amount of data available for each of those runs (and time you can spend) you could do all mentioned options in parallel. With a bacterial genome it should not be very time consuming affair.
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