Dear Mathias, welcome to BioStar. Unfortunately, I find that your questions does not totally satisfy the quality standards we have. This makes it very hard to get an answer that makes sense (unless you want a "yes use it ;)"). To improve your question please add some context, for example details about input data and procedures, organisms and the like, what is your biological question? Whole Genome Shotgun can involve a lot of different techniques, what is your lab-pipeline? Until, this problem is fixed I think it is better that your question is not answered, because the answer might involve a lot of guess work and might mislead you. Please feel free to comment on this and to improve your question by editing it.

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