getting data from american gut project

Question

[khorms]

Where can I download public data from American Gut project? (Not only mine, but all the available data?)

There are written at their FAQ page: "Are the results of the American Gut project going to be published?
Yes. After providing each volunteer with their specific data and depositing the data with the open-source Earth Microbiome Project, the research team will likely produce several peer-reviewed papers from the project as well as public presentations." But I still can't find download page...

Answer 1

[Istvan Albert]

Charles Warden has a guide here

http://cdwscience.blogspot.com/2013/10/how-to-download-your-american-gut-data.html

[khorms]

It's the right way, if I want to download the data only from my samples. And I asked: "(Not only mine, but all the available data?)"

[Istvan Albert]

You can follow a link to all the data like so http://www.ebi.ac.uk/ena/data/view/Taxon:408170

You can navigate and find the data and download individually.

Now if you want all the data you have to follow somewhat more complex steps to download all data from command line for example see How to download raw sequence data from GEO/SRA

I have not downloaded bulk data from EBI yet but it looks like you can export various pages as xml format, you'd expect that can parse that and extract the url from them.