Installing Modified PANDAseq

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 to my home directory and decompressed it.

cd ~
tar xzf RDP_Assembler.tgz

After that I followed the instructions in the README file to complete the installation.

cd RDP_Assembler/pandaseq
make clean

Test the installation by calling the help file.

cd ~
RDP_Assembler/pandaseq/pandaseq -h