velvet expected cov

[bioenvisage]

Can any one tell how to set the expected coverege parameter in velvet denovo assembly , if i have the illumina reads of 0.1x cov.

[spenthil]

Take a look at section 5.2 and 5.3 of the velvet manual:
5.2 Choice of a coverage cutoff (14)
5.3 Determining the expected coverage (16)

[bioenvisage]

hi ,thanks for your reply...From the manual it is stated that with reference to the graph the expected cov is calculated as 14x ,so what i understood is we should take the value of the highest peak.am I right ?

[spenthil]

You could always just use "-cov_cutoff auto" (take a look at the manual), but I prefer to avoid magic when possible.

I would make the graph and use it as a starting point, although I recommend then tweaking the parameters and seeing what you get (especially do'able since it is done in the second step, velvetg).