Video Tip of the Week: QIIME for Quantitative Insights Into Microbial Ecology

The other day I was watching scientists in my twittersphere discuss things they were observing at the American Society for Microbiology meeting (#ASM2013 for more chatter). I like to see what kinds of tools are being discussed at meetings–and twitter is quite useful for that–and this particular tweet caught my eye:

Microbial diversity is not an area that we’ve covered much before, so I thought it was time to have a look at QIIME, or Quantitative Insights Into Microbial Ecology, (pronounced Chime). I went over to their site and found that they have some really useful guidance on how one would get started to use QIIME. They say that the quickest way to get up and running is to install the Virtual Box, and they offer a video to show how that goes. So this week’s video is the QIIME Virtual Box setup.

They have another video of how you can get started using the Amazon cloud if that’s a direction you’d want to go as well.

There’s also a helpful text-based overview tutorial about how to get going with QIIME with the files you’d need to run the demonstration set. But there’s a number of other documentation pages and even more tutorials available for other aspects of the work you might want to do with their tools.

I haven’t used this tool myself, as it’s not an arena I’ve been researching or exploring to date. But it’s great to see researchers talk up QIIME, which indicates that it is very useful and it has support in the community. It’s also great to see that is under active development. You can keep up with their news and announcements on their blog. If you are doing microbial ecology or considering that direction for your research, check out QIIME.


Quick links:

Visit QIIME:

QIIME News and Announcements:


Caporaso, J., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F., Costello, E., Fierer, N., Peña, A., Goodrich, J., Gordon, J., Huttley, G., Kelley, S., Knights, D., Koenig, J., Ley, R., Lozupone, C., McDonald, D., Muegge, B., Pirrung, M., Reeder, J., Sevinsky, J., Turnbaugh, P., Walters, W., Widmann, J., Yatsunenko, T., Zaneveld, J., & Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data Nature Methods, 7 (5), 335-336 DOI: 10.1038/nmeth.f.303

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