What is 'reference=core_set_aligned.imputed.fasta"

hi, I am following ‘Esophageal community analysis’, thank you for your work.
but I cannot understand the file ’ reference=core_set_aligned.imputed.fasta '. Then the questions are included:

  1. what is ‘reference=core_set_aligned.imputed.fasta’ ?
  2. for similar analysis, how can I get this file, reference=core_set_aligned.imputed.fasta ?
    Thank you for your answer!

Hi there,

That pipeline is pretty old. I’d encourage you to instead follow the example for align.seqs on the MiSeq SOP page where you’ll use a SILVA reference alignment.