Taxonomic profiles

[cmorganl]

It would be beneficial to output a table with the relative and absolute abundances of taxa based on individual reference packages. This should be in long-table (tidy) format for simple integration with the tidyverse and other new visualization tools.

An example table could be:

Taxon	Lineage	Rank	RefPkg	Count	Relative_abundance
Euryarchaeota	Root; Archaea; Euryarchaeota	Phylum	McrA	28	0.03
Archaea	Root; Archaea	Kingdom	McrA	56	0.06

Eventually this multiple marker genes, such as universal single-copy markers, should be used together to produce better estimates of abundance.

[cmorganl]

This feature should be written to report summaries data at multiple scales - from SAGs and MAGs all the way to metagenomes.

When profiling SAGs and MAGs - this should essentially function with CheckM. The only thing standing in the way here is a critical number of reference packages: we have far too few reference packages for universal single copy marker genes.

Another requirement is defining the set of reference packages relevant to different clades.