Command for combining replicate samples

Good day!

I’m still not conversant on the commands of mothur. Just want to ask if there’s a command in which you can merge the replicate fasta files into one file and use it for further analysis. For example, in my case, I have 3 replicates (three data sets 16S V4 only) for my one sample . How can I make these replicates to just one representative file?
I am aware that there is a “merge.file” command. But is this the proper command?

Thank you very much

If you have three separate fasta files with no group information you can just concatenate them together. If you have a number of groups in your data and you want to merge a subset of them, the merge.groups command sounds like what you’re after.

Thank you so much.

I am currently running a 16S V4 amplicon analysis with MiSeq.
I am working on marine sponge samples transplanted in 3 different locations. I have 3 biological replicates (from DNA extraction to sequencing) for each location for a total of 9 samples.

I would like to compare the diversity between the three locations. So I am currently looking for the right way how to combine/sum/the reads for all the replicates in one in order to have unique data set per every location.

I completed the entire sequence-processing mothur pipeline and analyzing alpha/beta-diversity, phylogeny-based analyses. This was done with all 9 samples maintaining sample identity throughout all steps.

How would you process the replicates? Could you suggest me the best method to have a unique data set per location?

Is there a way to run the downstream analyses in a way that automatically combines replicates in order to compare the samples from three locations? Or do I need to combine replicates and end up with more sequences in each location, then repeat all sequence processing pipeline on 3 samples rather than 9?

Do you have ideas?

Thank you very much for your help.

I wouldn’t combine the replicates in mothur. Keep them separate so you can do analyses and discuss within and between region differences. With only 9 sample from 3 locations you’re going to be pretty limited in what analyses you can do, but for starters look at an NMS and see if your regions cluster together.