If we won’t know whether 1 sample = 1 donation I would call that out explicitly.

Looks like we only got SARS reads in two samples. This is a good candidate for validating with BLAST if there's time.

Also noteworthy that we saw a lot of anelloviridae in the Cebria Mendoza RNA MGS paper.

Maybe we have both RNA and DNA stages of anelloviridae get picked up, or maybe the RNA > cDNA sample prep just also got a bunch of anelloviridae DNA in it.

I would highlight/link the Cebria Mendoza paper here.

This is a great addition. I think it would actually be better to use the popular names in the above RA plot as well.

We may also have some data source internally at SB that has a mapping from NCBI taxonomic virus name to common name.

Why exclude Anelloviridae?

I think it would make sense to have a version of this plot with human reads removed as we discussed in the context of Cebria Mendoza paper.

Can the two QC sections be combined or are they stage specific?

I would make this a histogram. You can make two histograms - one for classified reads and one for all reads.

I still think making a histogram is the way to go for this plot

What is p_reads_max?