Question

Diversity Analysis From 454 Data (No 16S Amplicons)

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12.9 years ago

Iddo ▴ 230

So I have 454 sequences from several samples which I would like to compare. No separate 16S data was generated. What would be the best way for OTU diversity analysis? I do have MG-RAST results for these data, including GreenGenes/RDP/Silva. My concern is that the number of OTUs identified this way is rather small. And yes, I did denoise the data.

metagenomics • 2.9k views

ADD COMMENT • link updated 12.9 years ago by Casey Bergman 18k • written 12.9 years ago by Iddo ▴ 230

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Clarification, prompted by Casey's response: yes, i only have shotgun 454. I used MG-RAST, but very few 16S reads (300-800 / sample) hit the 16S database (GreenGenes). Thresholded with a minimum length of 100, 97% ID

ADD REPLY • link 12.9 years ago by Iddo ▴ 230

score 1 · Answer 1 · 2011-05-22

If I understand your question correctly, you have shotgun metagenomic 454 data. If so, three options spring to mind: MEGAN, CARMA and the Galaxy Metagenomics Workflow. I've had good luck running and modifying the latter, but don't have experience with the other systems. If these are on target, it would be good to know which works best for you.