Comments (3)
You can (should) only assembly the PE data. Single end data are not really appropriate for assembly. As for the PE data, how much do you have, how many individuals, etc?
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ok, there is a strong recommendation against doing that - there are some details in the paper, but basically polymorphism breaks the assembler, resulting in a less contiguous assembly. Typically the rec. is to use 1 individual for assembly, or 1 per treatment (biological) group. Minimizing individuals is really important for assembly.
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