vgnpc-plasmodium-spp

This repository contains preset configurations and scripts to automatically prepare vivaxGEN NGS-Pipeline environment directory for WGS analysis of Plasmodium species.

Installation

To setup a base environment directory and install the preset configuration, use the following stepsi (assuming PvP01_v2 reference genome):

1. activate a plain (base) NGS-Pipeline environment:

   $ [NGS_PIPELINE_INSTALL_DIR]/bin/activate
   

2. generate a base enviroment directory, for example: /data/WGS/Pv/PvP01_v2:

   $ ngs-pl setup-base-directory /data/WGS/Pv/PvP01_v2
   

   Tip

   To easily identify and differentiate between several base enviroment directory, it is recommended to use the reference genome name as part of the directory name

3. exit from the current enviroment and activate the new enviroment with the base enviroment directory:

   $ exit
   $ /data/WGS/Pv/PvP01_v2/activate
   

4. run the installation command for the intended settings, ie. for Plasmodium vivax PvP01_v2 (for other genomes, see Configuration Options section below):

   $ bash <(curl -L https://raw.githubusercontent.com/vivaxgen/vgnpc-plasmodium-spp/main/Pvivax/PvP01_v2/setup.sh)
   

Once installation process is completed successfully, the settings is ready to be used.

Configuration Options

The following are the installation commands for various reference genomes:

• Plasmodium vivax PvP01_v2:

  $ bash <(curl -L https://raw.githubusercontent.com/vivaxgen/vgnpc-plasmodium-spp/main/Pvivax/PvP01_v2/setup.sh)
  

• Plasmodium falciparum Pf3D7_v3:

  $ bash <(curl -L https://raw.githubusercontent.com/vivaxgen/vgnpc-plasmodium-spp/main/Pfalciparum/Pf3D7_v3/setup.sh)
  

• Plasmodium malariae PmUG01_v1:

  $ bash <(curl -L https://raw.githubusercontent.com/vivaxgen/vgnpc-plasmodium-spp/main/Pmalariae/PmUG01_v1/setup.sh)