Meneval : Meneco validation

Pipeline to run Meneco gapfilling tool and validate reactions proposed

Meneco Tool :

• Uses Meneco for GapFilling problem solving

S. Prigent et al., “Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks,” PLOS Computational Biology, vol. 13, no. 1, p. e1005276, Jan. 2017. https://doi.org/10.1371/journal.pcbi.1005276

GitHub : https://github.com/bioasp/meneco

Padmet Tool :

• Uses padmet networks format to manage all networks and padmets-utils functions.

Aite, M., Chevallier, M., Frioux, C., Trottier, C., Got, J., Cortés, M. P., Mendoza, S. N., Carrier, G., Dameron, O., Guillaudeux, N., Latorre, M., Loira, N., Markov, G. V., Maass, A., and Siegel, A. (2018). Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models. PLOS Computational Biology, 14(5), e1006146. https://doi.org/10.1371/journal.pcbi.1006146

GitHub : https://github.com/AuReMe/padmet

Requirements

Tools

• Must have ncbi-blast installed
  • with /bin/blastp
  • with /bin/tblastn

Python packages

• Pip packages required :

  • biopython >= 1.80
  • Meneco >= 2.0.2

• Cloned packages required :

  • aucomana : https://github.com/PaulineGHG/aucomana.git
  • padmet : https://github.com/AuReMe/padmet.git

Installation

NCBI-BLAST installation guide

https://www.ncbi.nlm.nih.gov/books/NBK569861/

Python packages

From this cloned repository :

bash install_dependencies.sh

Usages

Initialisation of project directories

meneval --init

Fill directories with the rights input files

Checking for input files

meneval --check

Generate supplementary input files

meneval --files

Gapfilling + Adding reactions with blastp hit

meneval --blastp

Gapfilling + Adding reactions from enrichment networks

meneval --enrich Group

(meneval --enrich all for considering all groups at once)

Gapfilling + Adding reactions left

meneval --fill

Removing reactions from enrichment networks

meneval --exclude

Run all steps from check step

meneval --workflow

Documentation

See the full documentation on wiki : https://github.com/PaulineGHG/Meneval/wiki