Originally posted by genetics_jo
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e.g.
The problem with Velvet (especially velvetg) is that it is not at all optimized for large genomes and the time to get to output can be unpredictable. Moreover, you can trust its contig step, but not its scaffolding. However, the contigs produced by Velvet can be easily done by SOAPdenovo2 or Minia in much less time. For example, with the hardware you are describing, SOAPdenovo2 will give you the output in hours, not days.
I know this is not the answer you asked for and you already mentioned about using other assemblers.
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