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The use of NGS platforms in WGS projects has improved the ability to rapidly determine reference genomes at the expense of overall assembly quality, especially in high copy and duplicated regions. The potato reference genome (The Potato Genome Sequencing Consortium, 2011) was successfully constructed using a combination of Illumina, 454 and 43 Sequencing Technologies and Their Use in Plant Biotechnology and Breeding Sanger reads. The implementation of hybrid methods using Roche 454 sequencing in combination with Sanger sequences has been effective in reducing overall cost and time to generate high-quality sequences in gene space regions (Rounsley, 2009).

This platform is based on Sequencing by Ligation (SbL) chemistry. SbL is a cyclic method but differs fundamentally from other cyclic NGS chemistries in its use of DNA ligase instead of polymerase, and two-baseencoded probes instead of individual bases as units. In SbL, a fluorescently labeled 2-base probe hybridizes to its complementary sequence adjacent to the primed template and ligated. Non-ligated probes are then washed away, followed by fluorescent detection. In SOLiD, every cycle (probe hybridization, ligation, detection, and probe cleavage) is repeated ten times to yield ten color calls spaced in five-base intervals.

In these cases, the resultant sequence can only be trusted if the confidence of the sequencing software is high enough. Phred scores, or quality scores are a widely accepted measure of the quality of DNA sequences. Phred scores are numerical estimates of error probability for a given base (Ewing & Green, 1998). Sequencing softwares each have their own scale for base scoring, and in these studies, the percent of high quality base calls in a sequence read-out (HQ%) is defined to be the percent of bases that have a quality score (phred score) greater than 40.

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