Question: Shotgun rarefactions - metagenomics (microbiome), MetaPhlAn2
gravatar for robert.kwapich
2.2 years ago by
United States/New York
robert.kwapich0 wrote:

Hi there community!

For some time I was working os 16S rRNA gene survey data. For this type of analysis one could use a rarefaction approach in order to have the same depth for each sample. Having different depths for each sample is sometimes referred to as searching 1 square meter of amazon jungle and 1 square kilometer of mojave desert and then comparing OTUs, taxons, etc... It is relatively easy to employ a rarefaction, as it is implemented in many software packages: qiime, mothur.

I have now a shotgun dataset - a whole genome sequencing of microbiome. For the start I am using a microbiome helper SOP. For taxonomy assignement I use MetaPhlAn2 approach. MetaPhlAn2 wiki doesn't even mention rarefaction. Since this step might be crucial for comparative analyses, where I have two groups/categories, each containing around 30 samples I want to have each sample as "standardized" as possible. Are there any approaches two rarefy WGS data? Is there a reason why I has not been yet implemented in for example MetaPhlAn2?

I'd be grateful for any insight, comments and suggestions.

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