sjtu-cgm/cpan

CPAN: A pan-genome based method for cancer genomics study

CPAN: A pan-genome based method for cancer genomics study

Introduction

Cancer genomics studies are essentially relied on the human reference genome. However, tens of million base-pairs are still missing in the current human reference genome sequence. Pan-genome analysis has been proved its powerful in plant and human et al. We expand the pan-genome analysis to study cancer genomes.

The CPAN homepage is http://cgm.sjtu.edu.cn/cpan/CPAN.html.

Installation

• Download the CPAN from github:

  git clone [email protected]:SJTU-CGM/CPAN.git
  

• Compile:

  make
  

  You will find executable files cpan et al. in bin/ directory.
• Add bin/ to PATH and add lib/ to LD_LIBRARY_PATH by adding the following text to ~/.bash_profile:

  export PATH=$PATH:/path/to/CPAN/bin/:
  export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/CPAN/lib/:
  export PERL5LIB=$PERL5LIB:/path/to/CPAN/lib/:
  

• And run:

  source ~/.bash_profile