Hello @emmlemore,
Looking at the tutorial you linked it seems like your math is good and that you have just a large amount of low frequency features. I don't think that it is super abnormal and your command looks good to me.
This step is definitely not specifically necessary. There are a lot of ways to go about filtering out contaminants. In general, selecting a minimum frequency threshold can be a trade-off between minimizing the number of false positive features (i.e., features that appear due to noise or sequencing errors) and retaining real signals in your data.
You could look into lowing your --p-min-frequency and also using a --p-min-samples parameter. This would allow you to select for samples that have a minimum frequency and appear in a minimum amount of samples.
Another option is to use something like decontam if you have control samples. Here is a forum post where they talk about methods for removing contaminants. Discussion: methods for removing contaminants and cross-talk - #10 by lewisNU
Hope that helps!
