Question: What Is The Best Pipeline For 16S Rna Metagenome Analysis?
5
gravatar for Pawel Szczesny
8.2 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

I'm doing lots of analysis on sequencing of 16S RNAs by 454. In addition to self-made tools I've used MEGAN quite extensively and plan to test QIIME soon. Given how many other options are there (I know about RDP and WATERS) I wonder what is currently the best pipeline for such task? (with 454 in in mind)

rrna metagenomics pipeline • 6.7k views
ADD COMMENTlink modified 3.9 years ago by Simply Bioinformatics110 • written 8.2 years ago by Pawel Szczesny3.2k
6
gravatar for Istvan Albert
8.2 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

Best is probably not the right qualifier. I really like the Mothur tool.

ADD COMMENTlink written 8.2 years ago by Istvan Albert ♦♦ 79k
2

Mothur is nothing short of a uniquely amazing tool. It is a single, self contained binary program yet it has everything: aligner, classifier, clusterer, filterer etc. (I've learned of it from this very site)

ADD REPLYlink written 8.2 years ago by Istvan Albert ♦♦ 79k

I've seen you'd recommended mothur at other question. I will definitely check it soon. Thanks.

ADD REPLYlink written 8.2 years ago by Pawel Szczesny3.2k

Hi Istvan,

can you still recommend mothur, or are there better tools available now?

I tried to use mothur, but it seems pretty obscure to me. There is no explanation of where to put my files and what files I need to create. Perhaps it's a problem of me not understanding it, but do you know any nice HowTo for that tool? 

 

Thank you for your help,

ADD REPLYlink written 3.7 years ago by daiefa123150

You'll need to work through a SOP (standard operating protocol) there are few for different platforms 454 and MiSeq for example: http://www.mothur.org/wiki/MiSeq_SOP

ADD REPLYlink written 3.7 years ago by Istvan Albert ♦♦ 79k
1
gravatar for Simply Bioinformatics
3.9 years ago by
WashingtonDC
Simply Bioinformatics110 wrote:

Mothur has one of the best tutorials around, if you are curious about each step of metagenome analysis
included brilliant step by step tutorial also 

https://www.mothur.org/wiki/MiSeq_SOP

https://www.mothur.org/wiki/454_SOP

ADD COMMENTlink modified 15 months ago • written 3.9 years ago by Simply Bioinformatics110
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