Illumina Hiseq data analysis

[kennlu]

Dear All:

I am just starting to deal with Metagenomic sequences. I got some previous data from others with illumina Hiseq paired end. I am looking for some software or pipeline to help me with analyzing. Any good suggestion with it?
I looked at MG-RAST, but as I got a very large data ( 16 Gb), is it fine to upload?
I was also looked at QIIME which I was using for 454 before, does QIIME handle with metagenomic data?
Or what other good software can be used?
Thank you for your help.

[Bachbioinfo]

Tools choice is depending on what you are looking as answers for biological questions.
For metagenomes analysis, I think, MG-RAST, RAMMCAP are best the tools to start for beginners in the goal to understand how to proceed the exploration of Organism/OTU/Phylotype abundance and Functional abundance. Hope this comment is useful