rarefaction method

Hello, everybody.

I am using a mothur pipeline (integrated in the SnowMan software https://epona.genome.tugraz.at/snowman/index.jsp
for analysis of metagenomic segquencing) :roll: . Does somebody know, what is a difference between
Mothur rarefaction method and RDP rarefaction method? Or at least what is pecific in rarefaction done by Mothur?

Thanks a lot :wink:

Iā€™m not sure what the RDP is doing, but rarefaction.single in mothur calculates the rarefaction by random sampling without replacement. Are you seeing differences? You can see how you can calculate the rarefaction curve without randomization on the rarefaction.single mothur wiki page. We use the randomization because it is much quicker than the analytical approach and gives very similar results.