different results by shhh.flows command

I run the shhh.flows command with the same parametes several times, but got a little different results each time.

I did’t understand the theory of this command and I’m not sure if the different results are reasonable.

Looking forward to your reply.


It’s reasonable, but the differences shouldn’t be huge. There is a clustering step to get going and there is some randomness there.

Thanks pschloss!
Moreover, are you familiar with the theory of this command and can you tell me more about it?

For most of the commands if you run the command with the citation option you’ll find a list of papers you can get on the command…

mothur > shhh.flows(citation)

Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.
Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009).  Accurate determination of microbial diversity from 454 pyrosequencing data.  Nat. Methods 6:639.

I appreciate your help very much. :slight_smile:

Hi, I have the similar problem ,the flow was 1779.According to the 454SOP, i should use the trim.seq(Using quality scores).but the result was not well, scrap was too much. I know you use the trim.flows.can you tell me the command lines,the minflows=?maxflows=?

You have to use flows=B for trim.flows and shhh.flows. Do you know which image processing pipeline your sequence provider used? If it was one of the long amplcons you can probably safely use 1000 flows