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- For ITS sequences some folks like to try and remove the ITS region using ITSxtractor tool. I do not do this because it seems a good way to introduce bias, is unnecessary now that we use ESVs, and is super slow. If someone disagrees, then I would be keen to hear why.
- Everything above assumes reads merge! If we have many biologically relevant reads that do not merge because read lengths output by the machine are too short. Then we have many additional considerations. Do we want to build in machinery that deals with unmerging reads on the fly?
- Should we concatenate forward and reverse reads.
- We will need to decide on a global trimming length, otherwise just one extra base on one side or the other of a read could lead to different ESVs
- Concatenation may complicate chimera detection, but I am not sure.
Once we have decided on how we want to process this info we will need to ensure the proper dependencies are installed on TETON. We might want to develop a singularity image so we can easily duplicate processing.