Subscribe to Journal
Get full journal access for 1 year
only $20.83 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
The repository at https://github.com/gavinmdouglas/picrust2_manuscript includes the processed data files that can be used to re-generate the figures and findings in this paper. The accession codes for all sequencing data used in this study are listed in the Supplementary Methods.
PICRUSt2 is available at https://github.com/picrust/picrust2. The Python and R code used for the analyses and database construction described in this paper are available online at https://github.com/gavinmdouglas/picrust2_manuscript.
Langille, M. G. I. et al. Nat. Biotechnol. 31, 814–821 (2013).
Iwai, S. et al. PLoS One 11, e0166104 (2016).
Jun, S. R. et al. BMC Res. Notes 8, 479 (2015).
Aßhauer, K. P., Wemheuer, B., Daniel, R. & Meinicke, P. Bioinformatics 31, 2882–2884 (2015).
Wemheuer, F. et al. Preprint at bioRxiv https://doi.org/10.1101/490037 (2018).
DeSantis, T. Z. et al. Appl. Environ. Microbiol. 72, 5069–5072 (2006).
Markowitz, V. M. et al. Nucleic Acids Res. 40 (D1), D115–D122 (2012).
Barbera, P. et al. Syst. Biol. 68, 365–369 (2019).
Czech, L. & Stamatakis, A. PLoS One 14, e0217050 (2019).
Louca, S. & Doebeli, M. Bioinformatics 34, 1053–1055 (2018).
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. Nucleic Acids Res. 40 (D1), D109–D114 (2012).
Narayan, N. R. et al. BMC Genomics 21, 56 (2020).
Caspi, R. et al. Nucleic Acids Res. 44 (D1), D471–D480 (2016).
Franzosa, E. A. et al. Nat. Methods 15, 962–968 (2018).
Chen, I.-M. A. et al. PLoS One 8, e54859 (2013).
We thank Zhenjiang Xu and Amy Chen for providing us access to data files used for testing and the default reference database. We also thank Heather McIntosh for help designing the pipeline flowchart. G.M.D. is funded by an NSERC CGS-D scholarship. V.J.M. is funded by an NIH/NIAAA Ruth L. Kirschstein National Research Service Award (F30 AA026527). J.R.Z. is supported by NSF IOS CAREER grant 1942647. S.Y.N. is funded by an NSERC Discovery Grant. C.H. is funded in part by NIH NIDDK grants U54DK102557 and R24DK110499. M.G.I.L. is funded by an NSERC Discovery Grant and an NSERC Collaborative Research Development with co-funding from GlaxoSmithKline to M.G.I.L. and J.R.B.
The authors declare no competing interests.
Editorial note: This article has been peer reviewed.
About this article
Cite this article
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
Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes
Computational and Structural Biotechnology Journal (2020)