Overview
NPLinker brings processed metabolomics and genomics together to prioritize hypotheses about which gene clusters produce detected natural products. It uses matched strain information and configurable scoring methods. Scored links are candidates for follow-up experiments, not confirmed biosynthetic assignments.
What can this tool do?
Common uses
- Prioritize gene-cluster and MS-feature links across microbial strains.
- Explore paired genomics and metabolomics datasets.
Scientific fit
Primary function
Multi-omics integration
Other functions
Molecular networking and chemical similarity, Visualization and reporting
Analysis types
Multi-omics, Untargeted metabolomics
Data compatibility
Inputs
Mass spectra, Feature or peak table, Sample metadata
Outputs
Statistical results, Human-readable report
Input formats
Supported GNPS network archives, antiSMASH GenBank regions and optional BiG-SCAPE outputs, Strain-mapping JSON
Output formats
Scored candidate links and webapp analysis views
Scope and considerations
Designed for
- Hypothesis generation from paired microbial genomics and MS metabolomics.
Not designed for
- Raw MS preprocessing or proof of a gene-cluster/product relationship.
Important requirements
- Matched strain identifiers connecting spectra and genomic regions.
- Supported GNPS outputs, antiSMASH results and configured dependencies, or a supported paired-omics project.
Considerations
- Missing strains, silent gene clusters and inconsistent sample naming can distort links.
- Choose compatible BiG-SCAPE and MIBiG versions; the documented example uses MIBiG 3.1, so do not assume that the newest MIBiG release is interchangeable.
Access and documentation
Open-source Python framework with a documented webapp interface. Current documentation requires Python 3.11 or later on Linux, macOS or Windows with WSL; external dependencies and reference databases require additional installation. Pin a release and reference-data versions.
License: Apache-2.0
Evidence and review
Official documentation, repository or archived release metadata and direct resource publications reviewed on 2026-09-12. Included for MS-based natural-product research. No installation, biological validation or independent benchmarking performed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Eldjarn GH, et al. Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions. PLOS Computational Biology 17, e1008920 (2021). doi:10.1371/journal.pcbi.1008920
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-12 · First committed entry
Add NPLinker and MIBiG with metabologenomics guidance
View change · Entry at this revision