HMSMCP2 - Metagenomic taxon abundances (MetaPhlAn2)
Taxonomic profiling of metagenomic reads - or "what microbes are in my community?" - was performed using MetaPhlAn2, which utilizes a library of clade-specific markers to provide pan-microbial profiling (http://huttenhower.sph.harvard.edu/metaphlan2). Strain characterization was performed using StrainPhlAn. The result is a tab-delimited matrix of species relative abundances per sample.