Appropriate choice of the 'exp_cov' (expected coverage) parameter in Velvet is very important to get an assembly right. In the following figure, we show data from a calculation on a set of reads taken from a 3Kb region of a genome, and reassembling them with varying exp_cov parameters. X-axis in the chart shows the exp_cov and y-axis shows the size of the largest scaffold assembled by Velvet.
http://www.homolog.us/blogs/2012/06/08/an-explanation-of-velvet-parameter-exp_cov/
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