Accelerating the quality control of genetic sequences through stream processing

Abstract

Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. However, all existing parallel tools for this purpose are based on a batch processing model, needing to have the complete genetic dataset before processing can even begin. This limitation clearly hinders quality control performance in those scenarios where the dataset must be downloaded from a remote repository and/or copied to a distributed file system for its parallel processing. In this paper we present SeQual-Stream, a Big Data tool that allows performing quality control on genomic datasets in a fast, distributed and scalable way. To do so, our tool relies on the Apache Spark framework and the Hadoop Distributed File System (HDFS) to fully exploit the stream paradigm and accelerate the preprocessing of large datasets as they are being downloaded and/or copied to HDFS. The experimental results have shown significant improvements when compared to a batch processing tool, providing a maximum speedup of 2.7x.