This repo is now archived, check the new version [https://github.com/evolozzy/NGS-Pipeline] which is under development

DESCRIPTION

These set of scripts is designed to align multiple samples of same species to a reference genome, then building consensus sequences and call variants.

USAGE

Download

git clone https://github.com/evolozzy/DNA-Alignment-Pipeline.git

Before using

• Make a subdirectory named Data in the folder containing your scripts and copy your files there, or change the line containing DATASOURCE in your PARAMETERS file, and set it to the folder that contains your data.
• If you have two or more sets of reads to merge keep them in separate directories in Data directory.
• Make sure you have your reference file.

Using

Setting the parameters

• Carefully change the PARAMETERS.
  • Set the REFERENCEFILE to the path to reference.
  • If you have two or more sets to merge, set MERGE to 1, otherwise set it to 0.
  • If you are running on multiple threads set THREADS to number of cores you want to use.
• Set the directories to be used in DIRECTORIES file.
  • If you're not running the scripts in the directory you have the scripts change the line containing WD to the path that contains your scripts.
• Install required software, and set PROGRAMPATHS.

Running

Inside the folder:

./runall.sh 

Or outside the folder:

/path/to/scripts/runall.sh

If you encounter any errors during the process and clean all the files created by the script:

./resetanalysis.sh