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Alpha & Beta diversity


update 2018: consider using the new version  → QIIME 2

→ Alpha diversity

How many taxa (OTU's) are detected in each sample?

mkdir Alpha
-i OTU/otu_table_mc2_w_tax_no_pynast_failures.biom -m chao1,shannon,observed_otus -o Alpha/alpha_diversity.csv

Difference in microbial composition between samples

# Normalize data (CSS normalization, instead of classical rarefaction)
# requires additional R packages -i OTU/otu_table_mc2_w_tax_no_pynast_failures.biom -a CSS -o OTU/otu_table_CSSnorm.biom

# Get beta diversity (Bray-Curtis sample to sample distance, and UniFrac distance)
# -t specifies phylogenetic distances used in UniFrac
# unweighted UniFrac does not take abundances into account -i OTU/otu_table_CSSnorm.biom -m bray_curtis,unweighted_unifrac -t OTU/rep_set.tre -o Beta_PCoA/

Result: distance matries for each distance measure

# PCoA plot of Beta diversity

# calculate PC's variances and sample position in PCoA plot -i Beta_PCoA/bray_curtis_otu_table_CSSnorm.txt -o Beta_PCoA/PCoA_data.txt

# Plot PCoA -i Beta_PCoA/PCoA_data.txt -m metadata.csv -o Beta_PCoA/
# results: Beta/beta_div_coords_2D_PCoA_plots.html (to open in web-browser)