I’m having trouble understanding the shhh.seqs command.
Is this a single-linkage algorithm? I’m assuming so because the default sigma parameter is set at 0.01. Can you change this default simply by adding “sigma=…”?
What data is used for the “shhh.seqs” command? In the description in the Mothur Commands it appears that all you need are a fasta file and a names file (and a groups file is optional). Is this raw sequencing data post-trimming or do the sequences need to be aligned? How is this different than pre.cluster?
I was at the December Mothur workshop and my notes from the workshop state that you give Mothur the rates at which certain sequence errors occur based on your mock community data, but I’m not sure how to extract those particular errors or how to feed them into this command.