I am rather new to NGS analysis so my question might be rather trivial.
I am currently running through the Miseq SOP, and have reached the steps where the seqs are clustered into OTUs using the cluster function.
When I read about the cluster function is states that.
Nearest neighbor: Each of the sequences within an OTU are at most X% distant from the most similar sequence in the OTU.
Furthest neighbor: All of the sequences within an OTU are at most X% distant from all of the other sequences within the OTU.
Average neighbor: This method is a middle ground between the other two algorithms.
Where the default is the Average neighbor option.
My question is then what is X? i.e. how many percent? and what is exactly the middle ground between the two first options?
Thanks in advance!