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454 (700nt) vs 2x100 nt Illumina for sequencing low complexity metagenome

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  • 454 (700nt) vs 2x100 nt Illumina for sequencing low complexity metagenome

    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.

  • #2
    What 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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    • #3
      Originally posted by msheldon View Post
      What domain are you trying to sequence. For low cost and higher throughput go with a 2x100 MiSeq run (2x300 would even be better).
      -Matt
      I'm not trying to sequence only the 16S rRNA, but rather the whole DNA and I hope to get 16S rRNA of sufficient length (via assembly?) to identify the microbes in there. Do you think that they assembly of Illumina 2x100 will be good enough for that?

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      • #4
        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.
        Last edited by nucacidhunter; 05-09-2014, 01:43 PM. Reason: correction

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