README.md

A repository containing the Daphnia populations variant calling pipeline

Lynch Lab Biodesign CME

Curated and updated by R. Taylor Raborn rtraborn@asu.edu

Initialized May 23, 2018

Running this code:

To run this code on your system, please do the following:

1. Clone the repository on your system as follows:

   git clone https://github.com/LynchLab/DaphniaVariantCall
   cd DaphniaVariantCall
   

2. Install NGSUtils on your system. Please consult INSTALL.txt for instructions.
3. Update the links in the pipeline (e.g. original_pipeline.sh) that you would like to test using your favorite text editor.
4. Execute the pipeline using the appropriate batch script on your cluster as follows:

   # To run the original pipeline (i.e. with Novoalign)
   # Please make changes to the pipeline (original_pipeline_novoalign.sh) and batch files as needed for your system.
   # The batch scripts are set up for the PBS job scheduler on IU Carbonate. 
   qsub original_batch_novoalign.sh
   # To run the Hisat2 pipeline:
   # Please make changes to the pipeline (hisat2_pipeline.sh) and batch files as needed for your system.
   qsub hisat2_batch.sh