Pyrosequencing Data Analysis

I do a data analysis of 454 pyrosequencing, and there is an analysis tool with us.
However, I read that Mothur done better.
The problem is that I can not seem to find myself in the literature: indeed, here is my basic tool in this way, we have regarding data and we must first make an RDP and then classify an OTU classification thanks to a blast is done on a database we have and finally Shannon and Chao statistics analysis…
I wish to change program and use mother to do these analysis.
Does anyone could explain to me what tools I need to take because I see a lot of packages and tools and I’m confused …

thank you

so I read carrefully the manual , so I don’t understand because in fisrt way,I don’t see where is the command of RDP classifier…
After, the blast based OTU classification, indeed I follow a tutorial (Analysis Example of 16s RNA gene for Beginners), I saw that at the 10 to do OTU it is this commandmothur > classify.seqs ? Because I have RDP database and I want to do the OTU classification by using a Blast against the RDP database.

Thank you

Sorry I post a lot of posts:
So , I did some research about the mothur program, I summarize my program pipeline and Mother.
My goal it’s to give to the program in entry a fasta file ( sequences to analyze), and I want to do a RDP classification with a RDP clasifier with a bayesian approach(I did’nt see the commad) , after an OTU classification by doing a blast or aother alignmet program against a RDP database.
By doing this, it classify for me cluster sequences with different similarities…
So finally I will do an analysis (Shanon and Chao)…

So I hope I summarize my demand …

Thank you

Have you looked at

thank you i did a pipeline of my work of all the commands, but I’m blocked at the first step.
We did a pyrosequencing with different studies like for human or rat in one pyrosequencing.
So I want to know if it’s possible after the quality check and before to start the OTU and RDP analysis, if we can chose to do just an analysis for human…
It can help to do the analysis by study…

Thank you

I have a question about the oligos file, I remark that in your example that we have just one tag or if with we have two tags like V1 and V3.
Do we build the oligos for each tag or we can put in the same oligos file.


you can have two primer sequences in your oligos file…

forward ATGCATGCATGC forwardPrimerA
forward ATGCAATTATGC forwardPrimerB