Please note that the QIIME database has become the Qiita database. Please follow the recently updated CoNet tutorial to obtain the latest version of the tutorial data from Qiita.

We are going to construct a network from samples collected in the arctic tundra during the summers of 2007 and 2008. The samples were sequenced with Roche FLX using primers for the V1V2 region of the 16S rDNA. The data set has been published in Environmental Microbiology 12(11), 2998-3006 (2010).

Data source
The data set can be downloaded from the QIIME database. The study identifier is: "Chu_arctic_soils". The account obtained for the QIIME database is also valid for the EMP database, which offers many more environmental 16S data sets.

Data preparation
In case you want to skip any of the steps described in this section, you can download all input files from here.

After unzipping of the QIIME file, you will find a biom file there, which you can convert into an OTU table using the biom tool available at If you use the following command:

biom convert -i study_104_closed_reference_otu_table.biom -o arctic_soils.txt -b --header-key taxonomy

you will obtain an OTU table that includes the lineages.
The QIIME zip file also contains a mapping file (study_104_mapping_file.txt). This mapping file lists for each sample a number of metadata, such as primers, run date etc. You can open this mapping file in Excel and copy the "#SampleID" column and the "PH" column into a new sheet, with the "#SampleID" column as first and the "PH" column as second column. Then remove the # from the "#SampleID", since # is interpreted as starting character of a comment line. You can then save the two columns into a tab-delimited file. We will refer to this file as "arctic_soils_features.txt".