MAGs_HPCpipeline

Parralelized pipeline (SLURM scheduler) for the generation of MAGs

Requirements

This pipeline requires a number of tools to function :

• Megahit
• MetaWrap
• QUAST
• CheckM

Installation

Conda environment

Create the assembly and metawrap environment ''' conda env create -f config/assembly_conda.yml conda env create -f config/metawrap_conda.yml '''

Databases to download

Download the databases for CheckM

''' cd MY_CHECKM_FOLDER wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz tar -xvf *.tar.gz rm *.gz

checkm data setRoot /path/to/your/dir/MY_CHECKM_FOLDER '''

Download the database for Kraken2

Visit the following page and download the Kraken2 database of interest https://github.com/BenLangmead/aws-indexes

Download the NCBI database

''' mkdir NCBI_nt cd NCBI_nt wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt_v4.*.tar.gz" for a in nt.*.tar.gz; do tar xzf $a; done

cd .. mkdir NCBI_tax cd NCBI_tax wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz tar -xvf taxdump.tar.gz '''

Install metawrap

• Clone the metawrap repository: git clone https://github.com/bxlab/metaWRAP.git

• Carefully configure the yourpath/metaWRAP/bin/config-metawrap file to it points to your desired database locations (you can modify this later). Follow the database configuration guide for details.

• Make metaWRAP executable by adding yourpath/metaWRAP/bin/ directory to to your $PATH. Either add the line PATH=yourpath/metaWRAP/bin/:$PATH to your ~/.bash_profile script, or copy over the contents of yourpath/metaWRAP/bin/ into a location already in your $PATH (such as /usr/bin/ or /miniconda2/bin/).

Other tools

Install QUAST from the source git repository: ''' git clone git@github.com:ablab/quast.git '''