Figure 1: Overview of the workflows used by QIIME, mothur and MG-RAST. Several steps are shared across the three pipelines (e.g. quality control, clustering, classification/assigning taxonomy). mothur has a unique step in which all sequences must be aligned to a template database and any sequences which do not overlap in the same space are removed from the analysis. OTU: Operational taxonomic unit; QC: Quality control.