I just finished reading "Sequence-specific error profile of Illumina sequencers" and I found it extremely interesting. It suggests that Illumina data suffers from quite serious systematic errors which may even affect SNP calls. I believe this will come as a surprise to the sequencing community. We are comfortable with 454 data having systematic homopolymeric tract problems, and with Illumina having high GC% issues, but I don't believe this particular issue has been described before.
I need to read it a few more times before I summarise my reaction, I will reply to my own question when I have.
What do you think about this paper? Do you believe there truly are such systemic issues with Illumina data? Is there any other explanation for the observed results?