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Old 03-26-2013, 02:45 PM   #1
Location: Auckland

Join Date: Sep 2011
Posts: 72
Default QIIME constraints and time to run for 16S Illumina

Hi, I am looking to help analyse a dataset that consists of a number of 16S (V3-V4) amplicons sequenced on a MiSeq (in triplicate) from a number of data points, with a view to getting the relative abundances of OTUs in the samples.
I was wondering a few things:
1) Are there any memory and / or processor-speed constraints when running QIIME, i.e. can you run every step in the pipeline on a reasonably good desktop (i7) with reasonable memory (8GB) in a reasonable time, or do you need to start using clusters or high-memory computers?
2)Any estimates on how long (for example) it would take to run a simple comparison between sample A and sample B (triplicated) to get relative abundances of OTUs and the appropriate pretty graphs?
3) Are there any common stumbling blocks that people tend to encounter, either in the setup or the running? I have already set it up natively on Ubuntu 12.04 LTS with only a few problems, and I understand the VDIs are good too.

Any help or feedback appreciated. Cross-posted in "Bioninformatics" since I'm not sure which is the most appropriate forum.
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