Modules Overview

FERMO functionality is separated in modules: each module has a certain functionality and takes certain parameters that modify its behavior. All modules are optional and can be switched on/off as desired.

Modules can be separated into two types:

• core_modules: run by default and must be turned off explicitly
• additional_modules: are disabled by default (e.g. because they need specific input files) and must be turned on explicitly

In the FERMO GUI, these parameters can be set using the input forms. If you are running FERMO in command line mode, see the section Parameters for information about setting up the parameter file.

core_modules

• Adduct Annotation
• Neutral Loss Annotation
• Fragment Annotation
• Spectral Similarity (Molecular) Networking

additional_modules

• Feature Filtering
• MS/MS Filtering
• Blank Assignment
• Group Assignment
• Phenotype Qualitative
• Phenotype Quantitative-Percentage
• Phenotype Quantitative-Concentration
• Spectral Library Annotation
• MS2Query Annotation
• antiSMASH KnownClusterBlast Annotation
• Feature Scores Calculation
• Sample Scores Calculation