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update 2018: consider using the new version  → QIIME 2

Analysis Steps QIIME 1

→ Install 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)
Taxa/otu_table_mc2_w_tax_no_pynast_failures_L6.txt (relative abundance taxa tables)

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