QIIME 1

Analysis Steps QIIME 1

1) Sequence pre-processing

Sequence quality control, remove primer, and join forward and revers reads.

Result: seqs.fna   (file containing all sequences)

2) OTU picking

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)

3) 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)

4) Statistical tests

Which microbes show the largest differences between environmental conditions?

Results: List of microbial taxa, ranked by p-values for statistical significance between the conditions.

5) Community stats: Alpha & Beta diversity

How different is the the microbial composition between samples?
Results: number of taxa per sample, PCoA plots