Parsing XSQ Files

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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

This command will generate a base-spaced file filename.fastq 

xsq-convert -s base
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