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Old 08-07-2013, 04:08 AM   #4
bstamps
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Location: University of Oklaoma

Join Date: Oct 2012
Posts: 40
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If you plan on only amplifying 500bp, I might ask why you aren't using Illumina and overlapping each read 50bp and then stitching the reads to get a final artificial read near 500bp (Or waiting a few months and getting 500bp when they move to 2x300). Not to knock pacbio, we use it for genome finishing, but amplicon sequencing for community analysis was made for the Illumina platform.

If you did plan on using the PacBio RS I would agree with flxlex and go with full length 16S. You would get considerably higher resolution of your community and take advantage of what PacBio does best (Long reads).
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