Just wondering what are the best tools out there (besides Krona, which I don't think is really that great) to visualize metagenomic data obtained from kraken2 output? Any R packages or other tools that can distill taxonomic info and abundance from multiple samples in a comprehensive manner?
Krona is nice for a quick view of the data but trying to manipulate it or make it look neater is quite difficult and virtually non-existent - especially when combining samples together.
My goal would be to determine abundance of species in my metagenomic samples, compare the samples (i.e. metagenomic communities in different sites), and the main phylums found in each community (i.e. archae, bacteria, nematodes, plant, etc..)
Thoughts? I would like to start this as a discussion and hopefully get some good tips on tools or methods that people have used successfully for this purpose.
I found this chunk of code on github which convert the output from kraken in a format (
matrix) that can be analyzed through metagenomeSeq. I think the same chunk can be used in conjunction with other packages (eg Phyloseq) because what you really need for this kind of analysis is a
matrixwith the abundance of each taxa across your samples.