Illumina is the leader platform today for Next Gneration Sequencing.
Its advantages are:
High data yields
Low price
Low error rate
Disadvantages:
Short reads
Not uniform coverage
The errors are not random
As this is the leading technology today, in Era7 Bionformatics we have a lot of experience analyzing data from Illumina sequencers and in designing many kind of sequencing projects involving Illumina platforms: