SNP detection for massively parallel whole-genome resequencing

Next-generation massively parallel sequencing technologies provide ultrahigh throughput at two orders of magnitude lower unit cost than capillary Sanger sequencing technology. One of the key applications of next-generation sequencing is studying genetic variation between individuals using whole-genome or target region resequencing. Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology. We designed this method by carefully considering the data quality, alignment, and experimental errors common to this technology. All of this information was integrated into a single quality score for each base under Bayesian theory to measure the…

• NN
  National Natural Science Foundation of China

  Awards: 90608010, 30221004, 90612019, 90403130, 30725008, 30392130
• L
  Lundbeckfonden
• HL
  H. Lundbeck A/S
• NH
  National High-tech Research and Development Program
• NK
  National Key Research and Development Program of China

  Awards: 2007CB815705, 2007CB815703, 2007CB815701