Engineering a high-performance SNP detection pipeline

We present Sprite, a bioinformatic data analysis pipeline for detecting single nucleotide polymorphisms (SNPs) in the human genome. A SNP detection pipeline for next-generation sequencing data uses several software tools, including tools for read preprocessing, read alignment, and SNP calling. We target end-to-end scalability and I/O efficiency in Sprite by merging tools in this pipeline and eliminating redundancies. A key component of our optimized pipeline is parsnip, a new parallel method and software tool for SNP calling. Experimental results on synthetic and real data sets indicate that the quality of results achieved by parsnip is comparable to state-of-the-art SNP calling software.