PANDAseq is a program for assembling or merging paired Illumina reads. RDP’s modified version improves the accuracy of assembly by performing a modified statistical analysis using the sequencer supplied Q scores to find the most likely region of overlap. A local installation of RDP’s modified PANDAseq is helpful for learning how to use the program and for developing pipeline scripts. I have included an example of its use in the workshop exercise under Command Line Initial Processing.
I suggest that you install modified PANDAseq in your home directory. This is because it apparently writes temporary files to sub-directories inside the directory in which it is installed. If you install it in /usr/local it will fail because it will not have write permissions for those sub-directories. I installed RDP’s modified version of PANDAseq in Ubuntu 16.04 LTS as follows.
First, I had to install libltdl-dev:
sudo apt-get update sudo apt-get install libltdl-dev
Then I downloaded the modified PANDAseq from http://rdp.cme.msu.edu/download/RDP_Assembler.tgz to my home directory and decompressed it.
cd ~ wget http://rdp.cme.msu.edu/download/RDP_Assembler.tgz tar xzf RDP_Assembler.tgz
After that I followed the instructions in the README file to complete the installation.
cd RDP_Assembler/pandaseq ./configure make clean make
Test the installation by calling the help file.
cd ~ RDP_Assembler/pandaseq/pandaseq -h