I am involved in a pilot experiment to examine the metagenomes of two environmental samples. This is largely exploratory at this point, with the intent being cataloging the genomic potential of the samples. Based on preliminary 16S clone libraries, approximately half of the community appears to be comprised of two OTUs.
Our budget is quite limited, and at this point I can do one lane of HiSeq 100 bp single-end sequencing. If it would be very beneficial, that could be stretched to 150 bp single-end, but I realize this will reduce the total number of reads from 180-200 million to ~140-150 million.
Another possibility that I am unfamiliar with is a MiSeq 2x300 run. Should this be a consideration?
Given the relatively low complexity, how likely is the assembly of a draft bacterial genome?
Thanks for your comments!
Our budget is quite limited, and at this point I can do one lane of HiSeq 100 bp single-end sequencing. If it would be very beneficial, that could be stretched to 150 bp single-end, but I realize this will reduce the total number of reads from 180-200 million to ~140-150 million.
Another possibility that I am unfamiliar with is a MiSeq 2x300 run. Should this be a consideration?
Given the relatively low complexity, how likely is the assembly of a draft bacterial genome?
Thanks for your comments!
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