Metrics to Compare Library Preparation

[Nighthawkrao77]

Hi,

I was wondering what measures users use on sequencing data to compare two sets of data. More specifically, if one were to compare TruSeq vs. NuGEN, for example, what metrics would be analyzed?

Coverage
Bias
Complexity....


And then, how would one decide whether one was better than the other? In other words, at what point would one say they are significantly different?

I know that's vague and nebulous but just trying to understand the important variables.

[Brian Bushnell]

Coverage bias and complexity, yes. Also:
Insert size distribution
Artifact contamination rate
Read error rate
Chimera rate
Cross-contamination rate
Total yield (of mapped reads)

What kind of project are you doing? If it's assembly, the ultimate answer is to assemble and see how good your assembly is.