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Shhh.flows (version 1.39.5.0)

flow - flowgram data:

Use sffinfo to generate flow data from an sff file and usually trimmed by trim.flows

Select Taxonomy from:

lookup - intensity value per homopolymer length:

table of the probability of observing an intensity value for a given homopolymer length

maxiter - maximum iterations to run (default 1000):

if the delta value does not first drop below the mindelta value.

mindelta - threshold for determining how much change in the flowgram correction is allowed:

default .000001 (10^-6)

cutoff - seed the expectation-maximizaton step:

default .01 (usually doesn't need to be changed)

sigma - the dispersion of the data in the expectation-maximization step of the algorithm:

default .06 (usually doesn't need to be changed)

large - split your flow file and process the pieces separately (default 10000):

order - flow order for nucleotides in the sequencer:

default is A, was TACG. Also accepts B or I

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The shhh.flows command is Pat Schloss's translation of Chris Quince's PyroNoise algorithm [1] from C to C++ with the incorporation of mothur's bells and whistles. Based on processing of test datasets provided by Quince, shhh.flows gives the same/similar output to AmpliconNoise. shhh.flows uses a expectation-maximization algorithm to correct flowgrams to identify the idealized form of each flowgram and translate that flowgram to a DNA sequence. Our testing has shown that when Titanium data are trimmed to 450 flows using trim.flows, shhh.flows provides the highest quality data for any other method available. In contrast, when we use the min/max number of flows suggested by Quince of 360/720, the error rate is not that great. This much improved error rate does come at a computational cost. Whereas the features in trim.seqs take on the order of minutes, shhh.flows can take on the order of hours. You will also need a lookup file that tells shhh.flows the probability of observing an intensity value for a given homopolymer length. You can get mothur-compatible files at: https://www.mothur.org/wiki/Lookup_files