Core microbiome identification
I have classified the organisms in my metagenomic shotgun sequencing data using metaphlan3. With metaphlan3 output, can I identify the core microbiome?
Or is there a way I can convert metaphlan3 output to phyloseq input format and use Core microbiome R package?
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vikasmh111 •
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import metaphlan3 data into phyloseq: https://github.com/wipperman/wipperman/blob/master/R/microbiota.R and What are the input files for lwaldron / metaphlanToPhyloseq.R ?.