(1) Background: DNA sequence alignment process is an essential step in genome analysis. BWA-MEM has been a prevalent single-node tool in genome alignment because of its high speed and accuracy. The exponentially generated genome data requiring a multi-node solution to handle large volumes of data currently remains a challenge. Spark is a ubiquitous big data platform that has been exploited to assist genome alignment in handling this challenge. Nonetheless, existing works that utilize Spark to optimize BWA-MEM suffer from higher overhead. (2) Methods: In this paper, we presented PipeMEM, a framework to accelerate BWA-MEM with lower overhead with the help of the pipe operation in Spark. We additionally proposed to use a pipeline structure and in-memory-computation to accelerate PipeMEM. (3) Results: Our experiments showed that, on paired-end alignment tasks, our framework had low overhead. In a multi-node environment, our framework, on average, was 2.27× faster compared with BWASpark (an alignment tool in Genome Analysis Toolkit (GATK)), and 2.33× faster compared with SparkBWA. (4) Conclusions: PipeMEM could accelerate BWA-MEM in the Spark environment with high performance and low overhead.
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