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Parallel-META 3

Version Release date

Contents

Introduction

Parallel-META 3 is a comprehensive and full-automatic computational toolkit for rapid data mining among microbiome datasets, with advanced features including sequence profiling and OTU picking, rRNA copy number calibration, functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing. Both metagenomic shotgun sequences and 16S/18S rRNA amplicon sequences are accepted.

System Requirement and dependency

Hardware Requirements

Parallel-META 3 only requires a standard computer with sufficient RAM to support the operations defined by a user. For typical users, this would be a computer with about 2 GB of RAM. For optimal performance, we recommend a computer with the following specs:

RAM: 8+ GB
CPU: 4+ cores, 3.3+ GHz/core

Software Requirements

OpenMP

OpenMP library is the C/C++ parallel computing library. Most Linux releases have OpenMP already been installed in the system. In Mac OS X, to install the compiler that supports OpenMP, we recommend using the Homebrew package manager:

brew install gcc

Rscript environment

For statistical analysis and pdf format output, Parallel-META 3 requires cran-R (http://cran.r-project.org/) 3.2 or higher for the execution of “.R” scripts. Then all packages could be automatically installed and updated by the Parallel-META 3 installer.

Vsearch (included in the package)

Vsearch has been integrated in the package. If you want to install/update manually, please download from https://sourceforge.net/projects/vsearch/ and put the “vsearch” to $ParallelMETA/Aligner/bin/.

HMMER 3 (3.0 or higher, included in the package)

HMMER3 has been integrated in the package. If you want to install/update manually, please download from http://www.hmmer.org/download.html and put the “hmmsearch” to $ParallelMETA/HMMER/bin/.

Installation guide

The latest release is available at: http://bioinfo.single-cell.cn/parallel-meta.html

Automatic Installation (recommended)

Now the Parallel-META provides a fully automatic installer for easy installation.

a. Extract the package:

tar –xzvf parallel-meta-3.tar.gz

b. Install

cd parallel-meta
source install.sh

The package should take less than 5 minutes to install on a computer with the specifications recommended above.

The example dataset could be found at “example” folder. Check the “example/Readme” for details about the demo run.

Manual Installation

If the automatic installer failed, Parallel-META 3 can still be installed manually.

a. Extract the package:

tar –xzvf parallel-meta-3.tar.gz

b. Configure the environment variables (default environment variable configuration file is located at “~/.bashrc” or “~/.bash_profile”)

export ParallelMETA=Path to Parallel-META 3
export PATH=”$PATH:$ParallelMETA/bin”
source ~/.bashrc

c. Install R packages

Rscript $ParallelMETA/Rscript/config.R

d. Compile the source code* (only required by the source code package):

cd parallel-meta
make

Citation

G. Jing, Z. Sun, H. Wang, Y. Gong, S. Huang, K. Ning, J. Xu, X. Su*. Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities. Scientific Reports, 2017

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A High Performance Microbiome Analysis Toolkit.

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