Fig. 1

Bioinformatics pipeline. While traditional metagenome analysis methods align reads with sequences in reference databases and perform taxonomy assignment directly, the method we used assembles reads into longer scaffolds before mapping to reference databases, and relies on lowest common ancestor (LCA) analysis to perform taxonomy assignment because scaffolds can potentially harbor multiple predicted genes. The longer length of scaffolds also makes it possible to classify scaffolds into one of the known, divergent, or novel categories based on their overall sequence similarity with reference databases. Publicly available tools used are annotated on top of boxes where used in the pipeline. Boxes in the center refer to publicly available databases used in the pipeline. NCBI: National Center for Biotechnology Information