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Research update

Software optimizations make variant calling 8 to 16 times faster

The imec ExaScience Life Lab developed a software tool – elPrep5 – for sequencing pipelines with variant calling. It produces results like established state-of-the-art genome analysis programs (SAMtools, Picard and GATK4®) but it speeds up the runtime by a factor 8 to 16, for both whole-exome and whole-genome data. 


ElPrep5 speeds up variant calling because it parallelizes and merges the execution of the sequencing pipeline steps while minimizing the number of data accesses to files. 

This software platform is interesting for pharma companies that use omics data to find new drug targets; for diagnostic and sequencing labs that want to speed up the customer experience; and for hospitals that want to implement personalized medicine and want to run analyses overnight. 

In this article, we show detailed results on runtimes, memory and disk space usage and scaling potential of the elPrep software. As an example, it was benchmarked on state-of-the-art infrastructure.