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- System requirement - What's the system requirement to install METABOLIC?
- Dependencies overview - What are the dependencies to install METABOLIC?
- Install instructions - What are the steps to properly install METABOLIC?
- Quick installation - What are the steps to quickly install METABOLIC?
- Full installation - What are the steps to fully install METABOLIC on the server?
- METABOLIC Usage - How to run METABOLIC-G and METABOLIC-C?
- METABOLIC output files - What are the outputs?
- METABOLIC version updates - What are the updates?
METabolic And BiogeOchemistry anaLyses In miCrobes
Current Version: 4.0
Tested on: Ubuntu 18.04.5 LTS (Linux 5.4.0-81-generic x86_64) (Sep 2021)
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 isolated strain 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, zczhou2017@gmail.com
Patricia Tran, ptran5@wisc.edu
Karthik Anantharaman, karthik@bact.wisc.edu
Anantharaman Microbiome Laboratory
Department of Bacteriology, University of Wisconsin–Madison
Copyright:
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
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