Complete Genomics vs Illumina, in other words.
Even most bioinformaticians aren’t going to have much familiarity with the topic. But as BGI starts to crank out more and more CG genomes, this comparison is going to loom large. Most of the data in the wild is currently Illumina, but that can’t stay the case forever; the CG data pool is going to grow rapidly, as BGI starts to shift all of their capacity into their acquisition.
The theme that seems to emerge again and again is the accuracy of CG vs the sensitivity of Illumina. And with “sensitivity”, I’m afraid I mean “infestation with false positives”.
| Number tested | Validated | Validation rate | |
| Both platforms | 20 | 20 | 100% |
| Illumina-specific | 15 | 2 | 13.3% |
| CG-specific | 18 | 17 | 94.4% |
http://www.nature.com/nbt/journal/v30/n1/abs/nbt.2065.html
http://mendeliandisorder.blogspot.com/2012/03/cliff-reid-on-cg-vs-illumina.html
If a fitting complement of CG controls can be located to offset Illumina control bias, the shift in our experimental design towards CG for cases may prove to be a large accuracy boon.
mindswarm 