FIG. 2.

In the bioinformatic pipeline for analysis of whole metagenome shotgun sequences, sequences are subjected to quality control by removing uncertain base calls and contaminant sequences. Alignment of sequence reads to reference genomes is used for calculating species abundance. De novo assembly is used to identify genes not present in public databases. Genes can be functionally annotated and mapped onto metabolic networks such as in KEGG. Abundance of genes and species are compared among groups, and associations with disease can be tested.