Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:

Huttenhower, C, Franzosa, E and Segata, N(2021). HMP2 IBD metagenome and metatranscriptome profiling. Bio-protocol Preprint. bio-protocol.org/prep1365.
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., Valles-Colomer, M., Weingart, G., Zhang, Y., Zolfo, M., Huttenhower, C., Franzosa, E. A. and Segata, N.(2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLIFE. DOI: 10.7554/eLife.65088