Hi @Sarah_McGrath - it looks like you are using QIIME 2 2017.11, but referencing a method from QIIME 2 2017.12. We recently renamed this method from merge-seq-data to merge-seqs, which would explain why you are seeing that error. As my momma taught me when I was but a wee child, "always remember to use the version of the docs that match the version of the software!" (well, maybe I am embellishing that memory a bit). So, you should be able to just tweak your command to use merge-seq-data instead, and then you are good to go! Good luck and keep us posted! 
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