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Difference between revisions of "Shhh.seqs"

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m (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 denoting program, SeqNoise.
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The [[shhh.seqs]] command is a mothur-based rewrite of Chris Quince's sequence denoising algorithm, SeqNoise [http://code.google.com/p/ampliconnoise/]. (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]].)
 
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==Default settings==
 
==Default settings==

Revision as of 22:42, 29 June 2012

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 - ...

Options

group

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

processors

sigma

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

Revisions

  • First introduced - version 1.23.0.