I've recently started looking into the different visual analytics tools out there to help with the NGS project I'll be working on in the coming weeks, and was wondering if I could get some thoughts/feedback on anyone's experience with such tools. So far I've identified DNA Nexus Apollo, BioTuring's BioVinci and Qiagen's CLC workbench as possible candidates, but I've heard that non genomics specific tools like Spotfire and Tableau can get the job done too.
Have a look at MEGA5. QIIME pipeline will be helpful in checking the quality of your sequences (i used version 1.9.0). UCHIME2 can help you identify and remove chimeric sequences and if you will be clustering your sequences into OTU's, UCLUST algorithm will do that for you. I think you will also need to look at GREENGENES database, R program Vegan and PhyloseqR packages. They will be all be helpful if you are thinking of assigning OTU's into different taxa, construct and visualise a phylogenetic tree. I hope this helps.
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