Pipeline to run Meneco gapfilling tool and validate reactions proposed
- 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
- 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
- Must have ncbi-blast installed
- with
/bin/blastp - with
/bin/tblastn
- with
-
Pip packages required :
biopython >= 1.80Meneco >= 2.0.2
-
Cloned packages required :
aucomana: https://github.com/PaulineGHG/aucomana.gitpadmet: https://github.com/AuReMe/padmet.git
https://www.ncbi.nlm.nih.gov/books/NBK569861/
From this cloned repository :
bash install_dependencies.sh
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
See the full documentation on wiki : https://github.com/PaulineGHG/Meneval/wiki