Evaluating the potential of new sequencing technologies for genotyping and variation discovery in human data.

Author(s): Carneiro, Mauricio and Russ, Carsten and Ross, Michael and Cahill, Patrick and Gabriel, Stacey and Nusbaum, Chad and DePristo, Mark A.

A first look at Pacific Biosciences RS data Pacific Biosciences technology provides a fundamentally new data type that provides the potential to overcome these limitations by providing significantly longer reads (now averaging >1kb), enabling more unique seeds for reference alignment. In addition, the lack of amplification in the library construction step avoids a common source of base composition bias. With these potential advantages in mind, we here evaluate the utility of the Pacific Biosciences RS platform for human medical resequencing projects by assessing the quality of the raw sequencing data, as well as its use for SNP discovery and genotyping using the Genome Analysis Toolkit (GATK).

Organization: Broad Institute
Year: 2012

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