NGS:pipeline

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Running the NGS pipeline on silverback.ucsd.edu

Familiarity with basic Linux command line is assumed

In order to make use of the NGS pipeline for HIV data on silverback.ucsd.edu one first needs to obtain an account on silverback.ucsd.edu

Preliminaries

Script locations

All of the scripts and support files for the pipeline reside in /opt/NGSpipeline. The scripts are written in Python, julia, and HyPhy batch language.

Installing Julia modules

One of the scripts

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