Fraction of reads incorporated in Velvet assemblies

[foram]

I was wondering what % of reads others are finding incorporated into velvet assemblies? I often see as low as 25-30% -- even with PE data, good (summary) quality scores, and high initial coverage. Is there an interpretation / reason for low % read incorporation?

I am using Illumina GA2 with reads from 45 - 76 bp and inserts from 300-600.

[Torst]

foram,
What velvetg parameters are you using?
What method did you use to determine only 30% of the reads were used?

[foram]

Hi Torst,

an error on my part. we are seeing 75%+ in assemblies.

thanks.

[Torst]

What velvetg parameters did you use?

Any use of coverage cutoffs, minimum contig lengths, insert distance tolerance parameters, etc. will throw away data at varying stages.