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Emerging high throughput next-generation sequencing technologies provide the ability to sequence genomes at high coverage and low cost; thus, enabling numerous biological applications. The raw error rate present in reads generated by these technologies is viewed as a limiting factor for error sensitive applications such as de novo assembly and rare variant detection. Here we present two error correction techniques enabled by the redundancy inherent in high coverage data: (i) a spectral alignment error correction method, that is applicable to base-space and color-space reads, and (ii) an exact call method that deconvolutes two orthogonal codes that are coming from two independent readings of the same DNA fragment. Reference can be an additional part of the convolutional code. This is enabled for the color-space reads generated by SOLiD 5500 System™. Both methods are part of the LifeScope™ software product by Life Technologies.