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.