References

If you find this pipeline helpful, please cite this GitHub Repository:

  1. Tran, P. Q., Michaelis, M. L., Qin, J.(2025). 16S rRNA gene pipeline. (link)

This workflow relies on the following softwares, please cite them as well:

  1. QIIME2: Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., … & Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852–857. https://doi.org/10.1038/s41587-019-0209-9
  2. DADA2: Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7), 581–583. https://doi.org/10.1038/nmeth.3869
  3. MAFFT: Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780. https://doi.org/10.1093/molbev/mst010
  4. FastTree: Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS ONE, 5(3), e9490. https://doi.org/10.1371/journal.pone.0009490
  5. Emperor: Vázquez-Baeza, Y., Pirrung, M., Gonzalez, A., & Knight, R. (2013). EMPeror: A tool for visualizing high-throughput microbial community data. GigaScience, 2(1), 16. https://doi.org/10.1186/2047-217X-2-16
  6. ANCOM-BC: Lin, H., Peddada, S. D. (2020). Analysis of compositions of microbiomes with bias correction. Nature Communications, 11, 3514. https://doi.org/10.1038/s41467-020-17303-4
  7. Silva Database: Robeson, M. S., II, O’Rourke, D. R., Kaehler, B. D., Ziemski, M., Dillon, M. R., Foster, J. T., & Bokulich, N. A. (2020). RESCRIPt: Reproducible sequence taxonomy reference database management for the masses. In bioRxiv. bioRxiv.
  8. GTDB Database: Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2021). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50(D1), D785–D794. 10.1093/nar/gkab776
  9. GreenGenes2 Database: McDonald, D., Jiang, Y., Balaban, M., Cantrell, K., Zhu, Q., Gonzalez, A., Morton, J. T., Nicolaou, G., Parks, D. H., Karst, S. M., Albertsen, M., Hugenholtz, P., DeSantis, T., Song, S. J., Bartko, A., Havulinna, A. S., Jousilahti, P., Cheng, S., Inouye, M., … Knight, R. (2023). Greengenes2 unifies microbial data in a single reference tree. Nat. Biotechnol.

Help and additional information:

Patricia Q. Tran, ptran5@wisc.edu, University of Wisconsin-Madison Get Help: