Diversity assessment based on taxonomic levels

[Paraqui]

In running this script

qiime diversity beta-group-significance \
	--i-distance-matrix core-metrics-results/bray_curtis_distance_matrix.qza \
	--m-metadata-file metadata-file.tsv \
	--m-metadata-column Description \
	--o-visualization core-metrics-results/bray-curtis-group-siqgnificance.qzv \
	--p-pairwise

Does this perform the bray-curtis comparison and PERMANOVA at the phylum level?
Is there anyway to examine the differences at other taxonomic levels like genus?
Does qiime2 have an option to run ANOSIM instead of PERMANOVA?

Thanks

[colinbrislawn (Colin J Brislawn)]

Good afternoon,

Great questions! Let's dive in.

@Paraqui

Does this perform the bray-curtis comparison and PERMANOVA at the phylum level?

This script just performs the permanova test on whatever distance matrix you provide. Based on the file name, this looks like a matrix of Bray Curtis dissimilarities.

@Paraqui

Is there anyway to examine the differences at other taxonomic levels like genus?

By default, these are calculated at the feature level (instead of grouping by phylum or grouping by genus, then calculating these dissimilarities). I would recommend keeping it like this.

@Paraqui

Does qiime2 have an option to run ANOSIM instead of PERMANOVA?

Yes! Check out the documentation to learn how, and let me know if you have any questions.

Colin