update 2018: consider using the new version → QIIME 2
Tutorials QIIME 1
Analysis Steps QIIME 1
Sequence quality control, remove primer, and join forward and revers reads.
Result: seqs.fna (file containing all sequences)
Get → OTU cluster of similar sequences and select a reference sequence
Result: otu_table_mc2_w_tax.biom (OTU abundance table of all samples, including taxonomy)
Which microbes are present and at which relative abundance?
Result: Taxa/taxa_summary_plots/bar_charts.html (to open in web-browser)
Which microbes show the largest differences between environmental conditions?
Results: List of microbial taxa, ranked by p-values for statistical significance between the conditions.
How different is the the microbial composition between samples?
Results: number of taxa per sample, PCoA plots