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Welcome to the METABOLIC wiki! This wiki page is in progress. Please refer to the main README page for the time being.
- Installation - how to install this software?
METabolic And BiogeOchemistry anaLyses In miCrobes
Current Version: 4.0
Tested on: Linux Ubuntu 16.04.6 LTS (GNU/Linux 4.15.0-101-generic x86_64) (June 2020)
This software enables the prediction of metabolic and biogeochemical functional trait profiles to any given genome datasets. These genome datasets can either be metagenome-assembled genomes (MAGs), single-cell amplified genomes (SAGs) or pure culture sequenced genomes. METABOLIC has two main implementations, which are METABOLIC-G and METABOLIC-C.
METABOLIC-G.pl allows for generation of metabolic profiles and biogeochemical cycling diagrams of input genomes and does not require input of sequencing reads. METABOLIC-C.pl generates the same output as METABOLIC-G.pl, but as it allows for the input of metagenomic read data, it will generate information pertaining to community metabolism. It can also calculate the genome coverage. The information is parsed and diagrams for elemental/biogeochemical cycling pathways (currently Nitrogen, Carbon, Sulfur and "other") are produced.
Zhichao Zhou, [email protected]
Patricia Tran, [email protected]
Karthik Anantharaman, [email protected]
Anantharaman Microbiome Laboratory
Department of Bacteriology, University of Wisconsin, Madison
If you are using this program, please consider citing our preprint, available on BioRxiv
Zhou Z, Tran P, Liu Y, Kieft K, Anantharaman K. "METABOLIC: A scalable high-throughput metabolic and biogeochemical functional trait profiler based on microbial genomes" (2019). BioRxiv doi: https://doi.org/10.1101/761643