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