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Revision as of 22:42, 29 June 2012 by Mbakker (Talk | contribs) (Provided additional background and updated web link, as well as link to shhh.flows.)

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The shhh.seqs command is a mothur-based rewrite of Chris Quince's sequence denoising algorithm, SeqNoise [1]. (Note: SeqNoise is one of two algorithms in the AmpliconNoise pipeline. The other, PyroNoise, runs first and takes as input the raw flowgrams. A mothur implementation of PyroNoise is available as shhh.flows.)

Default settings

The fasta and name parameters are required.

mothur > shhh.seqs(fasta=stool.trim.unique.good.filter.unique.fasta, name=stool.trim.unique.good.filter.names)

This will generate the following files:

  • stool.trim.unique.good.filter.unique.shhh.fasta - ...
  • stool.trim.unique.good.filter.unique.shhh.names - ...
  • stool.trim.unique.good.filter.unique.shhh.map - ...



mothur > shhh.seqs(fasta=stool.trim.unique.good.filter.unique.fasta, name=stool.trim.unique.good.filter.names, group=stool.good.groups)



The sigma parameter .... The default is 0.01.


  • First introduced - version 1.23.0.