Within the paper Workflow for Microbiome Data Analysis: from raw reads to community analyses under the header construct phylogenetic tree, what is the purpose of "seqtabNoC" within the code seq <- getSequences(seqtabNoC)? Is this a file? If so how do I gain access to it to assure my file is correctly formated?

It is the sequence table object, less chimeric sequences, i.e., chimeric sequences have been removed.

You can produce this object, seqtabNoC, by following the code from here: Construct sequence table and remove chimeras

In fact, I would encourage you to go through that entire workflow, from top to bottom.

Kevin