MGPipe: Automated analysis of metagenomics amplicons sequencing reads

MGPipe was developped to analyze sequencing reads from human or environmental samples and detect pathogenic bacteria of clinical and forense interest.

In the GermPLEX (auto) mode, the pipeline will automatically align and analyse the sequencing reads according to our reference database: Germplex DB.

Our modular pipeline also allows you to customize the alignment options, reference database and quality control or trim your sequencing reads before alignment.

Supervision:

@ Universidade Federal do Rio de Janeiro - UFRJ

Rosane Silva - silvaros@biof.ufrj.br

Development lead

Priscila da Silva Figueiredo Celestino Gomes - pfigueiredo@biof.ufrj.br

Contributors:

Diego Enry Barreto Gomes - dgomes@pq.cnpq.br
Victor Hugo Giordano Dias - victorhdias@biof.ufrj.br

Standard installation:

# Install Miniconda from:
https://docs.conda.io/en/latest/miniconda.html

# Download MGPipe repository
git clone https://github.com/priscila-fgomes/MGPipe.git

# Go to the program folder
cd MGPipe

# Install using the autoinstall script :)
./autoinstall

# Make sure you always activate MGPipe environment before running !
conda activate MGPipe

#Please add MGPipe to your $PATH. Add these lines to your .bashrc or .bash_profile
export MGPipe=${PWD}
export PATH=\$PATH:\${MGPipe}

# Automatic run, choose option 0. This mode compairs your reads to our GermPLEX Database
mgpipe.py
[0] - GermPLEX (Auto)

# Full parameter and modules list:
mgpipe.py -h

# To test, go to test folder and run "run_tests.bash"
cd test/
./run_tests.bash

Installation using Docker:

We prepared the mgpipe docker image which is easiest way to import and run the Pipeline, in this case you don't have to install all required packages.

For information on how to install and configure Docker on your system, visit : https://docs.docker.com/engine/install/

# Download MGPipe image
wget https://drive.google.com/file/d/1oPrZx_mqi-wSStkd1-w2a2fpOmf2GDAL/view?usp=sharing

# Import the image file into Docker:
docker load < mgpipe_latest.tar.gz

# Run docker file
docker run -it mgpipe:1.0

# Automatic run, choose option 0. This mode compairs your reads to our GermPLEX Database
mgpipe.py
[0] - GermPLEX (Auto)

# Full parameter and modules list:
mgpipe.py -h