Generation of consensus metabolic reconstructions and community-dependent gap-filling using COMMIT for communites sampled from Arabidopsis thaliana.
This repository contains all files used for community-dependent gap-filling and subsequent analysis of consensus genome-scale metabolic reconstructions for two soil communities (Bulgarelli et al. 2012, Schlaeppi et al. 2014).
The consensus reconstructions were generated by merging draft reconstructions from four different approaches:
- KBase (Arkin et al. 2018)
- RAVEN 2.0 (Wang et al. 2018)
- CarveMe (Machado et al. 2018)
- AuReMe (Aite et al. 2018) / Pathway Tools (Karp et al. 2016)
- Matlab (tested with versions R2017b and R2020b)
- CPLEX solver (tested with v12.9)
- R packages: pheatmap, wesanderson, scales, plotrix, igraph, ape
- COBRA toolbox v3.0
- HMMER (tested with v3.2.1)
- all settings can be changed in COMMIT/code/matlab/options.m
- the script COMMIT/code/matlab/commit.m contains the workflow for the publication
- the script COMMIT/code/matlab/gap_filling/run_iterative_gap_filling.m performs the conditional gap filling procedure of COMMIT
- the script COMMIT/code/matlab/gap_filling/gap_fill_individual_models.m performs gap-filling on the individual reconstructions without considering the community composition
Wendering P, Nikoloski Z (2022) COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PLOS Computational Biology 18(3): e1009906. https://doi.org/10.1371/journal.pcbi.1009906