use metaphlan on 16S sequences?

[paul]

Hello,

Can I run 16S illumina sequences through metaphlan, or is metaphlan only for shotgun sequencing of microbial communities?

Thanks,
-Paul

[Nicola Segata]

Hi Paul,

 MetaPhlAn cannot be used for 16S datasets.

thanks

Nicola

[Surya Saha]

Hi Paul,

If you have not already done so, I would strongly recommend QIIME or MOTHUR for analyzing your 16S data. They are also well documented.

-Surya

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Surya Saha

Department of Plant Pathology, 

Cornell University, NY, USA.

Sol Genomics Network, 

Boyce Thompson Institute, Ithaca, NY, USA.

http://www.linkedin.com/in/suryasaha

Twitter: https://twitter.com/SahaSurya

[jfg]

Hi all,

Is the incompatability with 16S mentioned on the MetaPhlan documentation? If not, could I suggest it be added as a small, three word note?

i.e. from https://bitbucket.org/biobakery/metaphlan2:

"Description
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data _(i.e. not 16S)_ with species level resolution."

I know it seems basic, but to those who are exploring bioinformatics, it would be an easy flag that they are looking at the wrong toolbox.

jfg