MARS uses Illumina’s BaseSpace to distribute data. Check out this how to if you have questions on getting your data off BaseSpace.
MARS standard 16S sequence processing is done using Kendra’s mothur batch file.
The old UConn MiSeq webpage
If you are analyzing amplicons you might want to check out my mothur batch processing file or my bash file. The batch file has more details of whats happening, the bash file is what I’m actively using on the UConn/UCH HPC1 so there may be slight differences.
If you are analyzing microbial genomes, check out the Computational Biology Core’s tutorial.
If you don’t want to deal with the BaseSpace web interface, you can use BaseMount (a CLI from Illumina). There is a for loop at the top of my bash file for downloading all files for a project and renaming each file with your sample name instead of MARS’ unique identifier for the sample.