Global biogeography of N2-fixing microbes: nifH amplicon database and analytics workflow

This figshare entry has the nifH ASV database described in Morando, Magasin et al. 2024. In this work we compiled published data for marine nitrogenase (nifH) amplicons that were sequenced on Illumina platforms and ran the datasets through our DADA2 nifH workflow. Briefly, the workflow entailed: detecting ASVs with a DADA2 pipeline customized for nifH; quality filtering and annotating ASVs using resources maintained by the Zehr and Turk-Kubo labs at UC Santa Cruz; and co-locating the samples with environmental data from the Simons Collaborative Marine Atlas Project (CMAP).The nifH ASV database in the 2024 publication is nifH_ASV_database_v2.tgz. An earlier version of the database (v1) is described in the preprint. Future versions will appear in figshare as new amplicon datasets become available.Software used to create the nifH ASV database:nifH-ASV-workflow in GitHub. This provides an overview of the workflow, a map of all included samples, and the scripts used to generate the nifH ASV database.nifH_amplicons_DADA2 in GitHub. This contains our DADA2 pipeline which processed samples by study. Then ASVs across all studies were processed together by the workflow. The pipeline can be used with amplicon data for genes other than nifH by specifying the primers and changing one parameter for how DADA2 error models are created.