Databases & Resources

NFixPlanet Database

The full NFixPlanet resource collection is available on Zenodo and includes the gene database, metagenome database, genome archive, HMM profiles, and associated metadata. The gene database was built by applying the NFixPlanet annotation pipeline on all genomes and contigs in SPIRE and proGenomes v3, and the metagenome database contains abundance profiles from 9,163 metagenomes processed with the NFixPlanet mapping pipeline.

View on Zenodo
NFixPlanet Toolkit

NFixPlanet is a Python package for running the NFixPlanet annotation and mapping pipelines. The package is available on GitHub and can be installed with pip or Bioconda.

View on GitHub View on Bioconda
Citation

If you use NFixPlanet in your research, please cite:

Ustick L, Roš H, Robbani SM, Schiller J, Fullam A, Mankowski A, Kim CY, Podlesny D, Seitz K, Schmidt TSB, Miravet-Verde S, Sunagawa S, Huerta-Cepas J, Kuhn M, Bork P. Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential. bioRxiv. 2026. doi.org/10.64898/2026.07.27.741065

View on bioRxiv

Workflows

NFixPlanet Annotation Pipeline

Identifies nitrogen fixation genes and operons in genome assemblies.

Predict open reading frames (ORFs) using Prodigal (optional if ORFs are provided)
Search ORFs against curated nitrogen fixation HMMs using HMMER
Retain the best HMM hit per ORF
Filter results for required genes on the same contig
Validate genomic context and operon structure
Resolve ambiguous assignments using neighboring genes
Outputs high-confidence nitrogen fixation gene annotations and operon assignments.

This workflow is designed for any nucleotide sequence, including genome assemblies, metagenome-assembled genomes (MAGs), or individual contigs.

NFixPlanet Mapping Pipeline

Quantifies diazotroph gene, genome, and taxonomic abundance from short-read metagenomes. This workflow integrates read mapping, abundance estimation, and taxonomic profiling into a single pipeline.

Perform read quality control
Map reads to the curated diazotroph reference database using CoverM
Calculate per-gene coverage
Estimate genome-level abundance
Normalize abundance by gene count
Assign taxonomy using reference taxonomy tables
Generate taxonomic abundance profiles