The EBI metagenomics portal has plenty of data on food metagenomes, including amplicon (16S RNA gene/16S RNA) targeted studies. Have a look: their analysis pipeline provides taxonomic assignment tables for individual runs and for the whole study in .tsv format.
Monthly Archives: September 2017
New version posted
I have included material on a new version of FMBN (2.0.3) in the versions page. I will start now collecting material for a new version. If you are interested to contribute contact me. You can download instructions and templates for submission here.
Why should you contribute?
Contributors receive new versions of FoodMicrobionet and R scripts as soon as they are ready and are entitled to assistance in the use of the software for data extraction and analysis. In general, I am more inclined to use data received from authors of published papers (and include the data in FoodMicrobionet in a way that matches what has been published). However, we are also including material obtained by directly processing projects deposited in SRA and ENA with a standardised pipeline. The whole issue about FMBN is to make data (which in most cases are already deposited in public repositories) freely available in an easy(ish) to use format. So, why bother contributing if you can get data and scripts anyway? Well, as a contributor you get the data and scripts 6-9 months before they are made public and you can freely use them for your metastudies and reviews. The only thing we require is that you cite the source and the relevant published papers.