I have a low complexity archaeal enrichment for which I want a quick (and cheap) look inside (metabolic potential) and importantly, to identity its archaeal members based on 16S (e.g.) its members. Which would you recommend: 454 with 700 nt reads, or Illumina, 2x100 reads. I heard that Illumina is better, but i this case I'm not sure.
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Originally posted by msheldon View PostWhat domain are you trying to sequence. For low cost and higher throughput go with a 2x100 MiSeq run (2x300 would even be better).
-Matt
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I assume by sequencing you want to assemble contigs and search for presence of genes involved in metabolic pathway of interest and also identify archaeal species. 16S region is not divergent enough (at least for bacteria) for correct assembly from short reads. I would prefer MiSeq 2x300 reads over 454 long reads because of accuracy and cost effectiveness.
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