Figure 2.

Impact of analysis choices on virome composition. Each step of a virome analysis protocol presents different options, each of which may affect the final outcome. (A) Sample type. (B) Physical separation of VLPs. (C) Amplification of virome DNA can preferentially amplify certain viral taxa (see Figure 3). (D) Sequencing chemistry, depth of sequencing and read length. (E) Assembly programs vary significantly in their ability to assemble virome data (see Figure 3). Reporting on the composition of viral sequences with homology to reference databases excludes the unknown majority of the virome. Clustering viral sequences by gene composition offers a promising alternative to database dependent methods by addressing high levels of sequence divergence in viral genomes.