## Overview

This document provides a quality assessment of Genome Analyzer results. The assessment is meant to complement, rather than replace, quality assessment available from the Genome Analyzer and its documentation. The narrative interpretation is based on experience of the package maintainer. It is applicable to results from the 'Genome Analyzer' hardware single-end module, configured to scan 300 tiles per lane. The 'control' results refered to below are from analysis of PhiX-174 sequence provided by Illumina.

The R code used in this document can be read into your own session with the following:

      fl <- system.file("scripts", "qa_utilities.R", package="ShortRead")
      source(fl)