In articles and other publications, please cite Nephele as follows:
Weber N., et al. (2018) Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis. Bioinformatics, 34(8): 1411–1413. https://doi.org/10.1093/bioinformatics/btx617
Alternatively, use the following acknowledgement:
This study used the Nephele platform from the National Institute of Allergy and Infectious Diseases (NIAID) Office of Cyber Infrastructure and Computational Biology (OCICB) in Bethesda, MD.
Please also report the publication of articles which made use of Nephele by providing the reference in an email to the Nephele Project Team.
Please cite the appropriate pipeline reference(s) along with citing Nephele. Additional references are available on each pipeline's help page.
Pre-processing QC
Nephele uses different tools depending on which options you choose for this pipeline. See the Pre-processing QC pipeline's reference list.
mothur
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ,
Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, platform-independent,
community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537-41.
QIIME 1
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Gonzalez Pena A, Goodrich JK,
Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M,
Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis
of high-throughput community sequencing data. Nature Methods. 2010;7(5):335-336.,
qiime.org
QIIME 1 uses multiple open source software tools that should also be cited. Please see "Citing QIIME" on the above link for details.
DADA2 & DADA2 ITS
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA and Holmes SP (2016). "DADA2: High-resolution sample inference from Illumina amplicon data." Nature Methods, 13, pp. 581-583. doi: 10.1038/nmeth.3869.
See the DADA2 pipeline's references section or DADA2 ITS pipeline's references section for citations of specific databases and taxonomic classifiers, which depend on the user options chosen.
BioBakery pipeline (WGS)
The bioBakery WGS pipeline is based on the bioBakery workflows developed by the Huttenhower Lab:
McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, ... Huttenhower, C. (n.d.).
bioBakery: a meta'omic analysis environment. Bioinformatics 2018;34(7):1235-1237.
doi: https://doi.org/10.1093/bioinformatics/btx754.
Downstream analysis
Bolyen, Evan, et al. "Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2." Nature Biotechnology, July 2019, doi:10.1038/s41587-019-0209-9.
QIIME 2 uses multiple plugins that should also be cited individually if their results are used. Please see the Downstream analysis pipeline's references section as well as the links to the individual plugin methods in the pipeline steps.
QIIME 2
See the QIIME 2 pipeline's reference list.
SARS-COV-2
See the SARS-COV-2 pipeline's reference list.
WGSA
Angelova AG, et al. (2023). WGSA2 workflow - a tutorial. https://dx.doi.org/10.17504/protocols.io.n92ldm98xl5b/v1
See the WGSA pipeline's reference list.
PICRUSt2
PICRUSt2: Douglas, G.M., Maffei, V.J., Zaneveld, J.R. et al. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol 38, 685–688 (2020).
https://doi.org/10.1038/s41587-020-0548-6
Morpheus, https://software.broadinstitute.org/morpheus
For a list of citations associated with Nephele pipelines, please visit our NCBI PubMed Collection.