| name | metabolic |
| description | METABOLIC (AnantharamanLab) — high-throughput metabolic and biogeochemical trait profiling of MAGs/SAGs/isolates with C, N, S, and other elemental cycle diagrams (METABOLIC-G genomes-only; METABOLIC-C with reads / community networks). Use for multi-element cycling potential and MW-score networks. Upstream: https://github.com/AnantharamanLab/METABOLIC. Route via element-cycling. Fe-deep dive → fegenie; S entropy scores → mebs.
|
| license | MIT |
| category | analysis-tools |
| tags | ["METABOLIC","biogeochemistry","C","N","S","P","element-cycling","MAG"] |
| upstream | https://github.com/AnantharamanLab/METABOLIC |
| stage | mining |
METABOLIC
Upstream: AnantharamanLab/METABOLIC
Citation
Zhou, Z. et al. METABOLIC: high-throughput profiling of microbial genomes for
functional traits, metabolism, biogeochemistry, and community-scale functional
networks. Microbiome 10, 33 (2022).
https://doi.org/10.1186/s40168-021-01213-8
See also docs/references.md.
Analytical thinking
METABOLIC annotates genomes then draws biogeochemical cycle summaries —
commonly carbon (C), nitrogen (N), sulfur (S), plus other
transformations (H₂, metals/metalloids as covered by the HMM/KOfam template).
Use METABOLIC-G.pl without reads; METABOLIC-C.pl when metagenomic reads
enable coverage / community contribution diagrams (MW-score, Sankey, networks).
| Element focus | Role of METABOLIC |
|---|
| C | Fixation and organic C transformations |
| N | Fixation, nitrification, denitrification, anammox, … |
| S | Oxidative/reductive sulfur steps |
| P / H₂ / others | Via modules / “other” cycle panels — pin template version |
| Fe | Present at trait level; deep Fe → fegenie |
Heavy DB install (KOfam etc.). Pin METABOLIC version, module cutoff, and DB.
How to run
perl METABOLIC-G.pl -t 40 -m-cutoff 0.75 -in-gn Genome_files -kofam-db full -o METABOLIC_out
Decision tree
Multi-element biogeochem on MAGs?
├─ Genomes ± reads → metabolic (G or C)
├─ S-centric entropy → mebs
├─ Fe genes/siderophores → fegenie
└─ Distilled sheets → dram
Related skills
element-cycling · mebs · fegenie · dram · kegg · gapseq ·
microbial-mining · tool-selection
