shhh.seqs

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

Default processors=Autodetect number of available processors and use all available.

sigma

The sigma parameter .… The default is 0.01.

Revisions

• 1.23.0 First introduced.
• 1.33.0 Improved work balance load between processors.
• 1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.