What Is The Best Pipeline For 16S Rna Metagenome Analysis?

Question

[Pawel Szczesny]

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)

Answer 1

[Istvan Albert]

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

[Istvan Albert]

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)

[Pawel Szczesny]

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

[daiefa123]

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,

[Istvan Albert]

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

Answer 2

[Simply Bioinformatics]

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