The bioBakery workflows uses the [AnADAMA](http://huttenhower.sph.harvard.edu/anadama) enviroment for reproducible analyses to process shotgun metagenomic and metatranscriptomic sequencing data, including sequence quality control and host read depletion (KNEADdata), taxonomic profiling (MetaPhlAn{33944776}), functional profiling (HUMAnN{33944776}), and strain profiling (StrainPhlAn). [MetaPhlAn](http://huttenhower.sph.harvard.edu/metaphlan) provides pan-microbial (bacterial, archaeal, viral, and eukaryotic) taxonomic profiling, allowing the quantification of individual species and strains across metagenomic samples. [HUMAnN](http://huttenhower.sph.harvard.edu/humann) provides species-specific functional profiles and pathway reconstructions using the UniRef{17379688} orthologous gene family catalog and MetaCyc{24225315}.
