Gempipe documentation

Gempipe is a tool for drafting, curating and analyzing pan and multi-strain genome-scale metabolic models (GSMMs or GEMs).

• Introduction

• How to install

• Part 1: gempipe recon
  • Starting from genomes
  • Starting from species taxids
  • Filtering the genomes
  • Starting from proteomes
  • Starting from genbanks
  • Creation of a PAM
  • Gene recovery
  • Draft pan-GSMM reference-free reconstruction
  • Draft pan-GSMM expanded reference-based reconstruction
  • Transport reactions expansion with TCDB
  • Annotation and duplicates removal
  • Output files
• Part 2: manual curation
• Part 3: gempipe derive
  • Deriving strain-specific models
  • Gap-filling strain-specific models
  • Biolog® PM simulations
  • Strain-specific screenings
  • Deriving species-specific models
  • Output files
• Part 4: multi-strain analysis
• gempipe autopilot

• How to cite