Parsing XSQ Files
Using NGS Plumbing
Installation
If not already installed install the ngs_plumbing package, entering your computer password when prompted. You probably need HDF5 and h5py installed as well.
sudo pip install ngs_plumbing
Usage
Once installed, use the xsq-convert function from the command line. The following command will convert a filename.xsq file into a colorspaced filename.fastq file
xsq-convert -s color filename.xsq
This command will generate a base-spaced file filename.fastq
xsq-convert -s base filename.xsq