Looking through the recent paper by Quail et al* I noticed this ..
454-like amplicon sequencing on the Illumina? Be interested to hear if anyone has tried this?
I guess you could build in the standard Illumina sequenicng primer into your amplicon if you didnt want to sequence with custom primers ...
* http://www.nature.com/nmeth/journal/...meth.1270.html
To avoid unnecessary PCR amplification steps, which would potentially exacerbate biases, we can perform extremely deep sequencing of short amplicons using locus- specific primers that possess tails that can hybridize to the oligos tethered to the flowcell surface. The tailless forward and reverse oligos are then used as primers in the sequencing steps (Supplementary Protocol 10 online).
I guess you could build in the standard Illumina sequenicng primer into your amplicon if you didnt want to sequence with custom primers ...
* http://www.nature.com/nmeth/journal/...meth.1270.html
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