Documentation for gapseq

gapseq is a program for the prediction and analysis of metabolic pathways and genome-scale networks. This documentation covers software installation, basic use cases and sample workflows with focus on application. For details on the biological and technical background please check the gapseq publication. In addition, the source is available at github.

Installation

• Installation
  • Ubuntu/Debian/Mint
  • Centos/Fedora/RHEL
  • MacOS
  • conda
  • SBML support
  • cplex solver support
  • Troubleshooting

Usage

• Basic usage
  • Pathway and transporter prediction
  • Draft network reconstruction and gapfilling
• Parameters for network reconstruction
  • Absence/presence of reactions
  • Parameter -b in gapseq find and gapseq find-transporter
  • Parameters -l and -u in gapseq draft
  • Parameter -b in gapseq fill
• Growth medium definition
  • Growth medium file format
  • List of potential nutrients
  • Predicting a growth medium
• Output files
  • gapseq find
  • gapseq find-transport
  • gapseq draft
  • gapseq fill
• Adapting models
  • Change reactions or entire pathways of a model
  • Modify growth conditions of a model
• panDraft: species-level models
  • Build the panDraft model of a species
  • Integration with further features of gapseq

Database

• Biochemistry
  • List of database-specific compound definitions
• Biomass Reactions
  • Biomass reaction presets
  • User-defined biomass reactions

Tutorials

• Cross-feeding of two gastrointestinal bacteria
• Lactic acid bacteria in yogurt production
• Reconstruction of metabolic networks for archaea
• Reaction tracing

FAQ

• What kind of organisms are supported by gapseq?
• What are the output files of gapseq?
• What are all these RDS output files for?