Illumina Paired-End Sequencing Data Processing

The ongoing rapid cost reduction of Illumina paired-end sequencing has resulted in the increasingly common use of this technology for a wide range of genomic studies, and the volume of such data is growing exponentially. Generating high-quality variant calls from raw sequence data requires numerous data processing steps using multiple tools in complex pipelines. Typically, the first step in this analysis is the alignment of the sequence data to a reference genome, followed by the removal of duplicate read-pairs that arise as artifacts either during polymerase chain reaction amplification or sequencing. This is an important pipeline step, as failure to remove duplicate measurements can result in biased downstream analyses.