Skip to content
Zhichao Zhou edited this page Oct 11, 2021 · 28 revisions

Wellcome to METABOLIC Wiki page

Introduction

Installation

Running METABOLIC

About:

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.

Contact:

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/.

Citation:

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
Clone this wiki locally