Order of commands for taxonomy analysis

I was wondering if you could please check the below order to successfully do taxonomy analysis. I checked the tutorials but I think normalization is not part of the process in the tutorials. Thanks!

  1. Transform fastq to qza format
  2. Quality control (e.g., dada2)
  3. Making feature table
  4. filter table
  5. normalize
  6. classifier
  7. making biom for Galaxy


I have a question about the steps that need to be done for taxonomy analysis. After using a classifier (e.g., SILVA), we need to filter data. Do we need to NORMALIZE taxonomy after filtering? If yes, which command helps for normalization. I checked the tutorials, but I did not see any related command for normalization.


Hello Zahra,

Let's start with this flow chart from the Qiime2 overview:

Note that analysis is a graph / network / flowchart, so it's non-linear.

These are separate steps so order does not matter.

  • If you want to make a PCoA plot, you probably need to normalize but you don't need taxonomy.
  • If you want to build a phylogenic tree of your ASVs, you don't need normalization and you don't need taxonomy!

See the examples from this section of the PD-Mouse tutorial :mouse2:
Search for 'rarefaction' to see each time this normalization method is discussed.

Some methods like gneiss handel normalization on their own and don't need an upstream step. This is why it's good to view analysis as branching paths, not a straight line with a fixed order. :palm_tree: