Hi,

I would greatly appreciate some help with my problem.

I have just assembled denovo a genome from Illumina 100bp paired end reads, using SOAPdenovo2 and then GapCloser.

My total scaffold length is 1,062,995,336 base pairs (from 207528 scaffolds) and my haploid genome is approximately 1.2 Gb. From this I calculate a percentage coverage of 104%?

Have I calculated coverage incorrectly, or should I have filtered short scaffolds? I am unsure why the coverage is greater than 100%?

Thanks very much for any help

Alison

How did you calculate 104%? from what you've said, your assembly is 1.06 Gb in size, and you are expecting 1.2 Gb so wouldn't your coverage be 88% (1.06/1.2)?