The nifD database (version 1.1.0) for the DADA2 pipeline is based on the same principles and methods as the nifH database for DADA2 (M. A. Moynihan et al., 2023). Briefly, Arbitrator 2023 (Heller et al., 2014) were used to construct an ARB database for nifD. nifD ARB database were exported to XML followed by updating sequences taxonomic annotations according to NCBI.
References:
- Heller, P., Tripp, H. J., Turk-Kubo, K., & Zehr, J. P. (2014). ARBitrator: A software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank.
- Bioinformatics, btu417.NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018;46(D1):D8-D13. doi:10.1093/nar/gkx1095
- M. A. Moynihan & C. Furbo Reeder 2023. nifHdada2 GitHub repository, v2.0.5. Zenodo. http://doi.org/10.5281/zenodo.7996213
Acknowledgement:
We acknowledge the support from Simons Foundation (Award#: 824763), the National Science Foundation PRFP program (Award #2205993), NOTION by BNP Paribas Fundation for Climate and Biodiversity, MANIOC by Aix-Marseille University, and DINDE by CEFIPRA and IDEFIX. We would also like to thank Jonathan Magasin for helpful discussions.
Please cite:
C. Furbo Reeder, M. A. Moynihan & S. Chowdhury 2023. nifDdada2 GitHub repository, v1.1.0. DOI 10.5281/zenodo.10124357