Applying the so-called GS FLX++ technology for 454, some company claims that can now deliver approx one million reads with max single read length of up to 1100 base pairs (bp), resulting in up to 800 Mbp of sequence data per full run. On the other hand Illumina MiSeq sequencing offers sets with which 16S rRNA amplicons are generated that cover different variable regions with 2 x 300 bp paired-end reads. I was wondering should I go with Illumina MiSeq or the 454 sequencer, if I want to plan for a large experiment of 300 intestine samples over the next 1 month to identify the population of bacterial species living in each sample.
The question really is the depth you wanna touch for each sample.
If you dont have either machine but intend to buy one, I might suggest 454 for as its more suited to amplicon sequencing, Miseq has certain issues let us say in that area.
But if you want to go really deep then Miseq is certainly for you, the new chemistry does provide long reads with paired ends.
Do remember to calculate the computational cost for such endeavors. As 454 would need more input for denoising algorithms.
Goood luck.
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