Sentieon’s Secondary Analysis Tools Explained

         September 12, 2017

We find ourselves talking about our partnership with Sentieon, a lot! More specifically, we are always extolling the powerful, comprehensive genomic data analysis solution we are able to offer our clients. Sentieon’s Secondary Analysis Suite made a significant improvement in runtime over BWA-MEM, GATK, Mutect, and MuTect2 while providing deterministic and identical results. Here are two fantastic white papers that cover the improvements Sentieon’s suite provides in more detail:

Sentieon DNA Pipeline for Variant Detection

The software-only solution, over 20× faster than GATK 3.3 with identical results

“Recent advances in next-generation sequencing (NGS) technologies have dramatically increased the rate of data output while significantly reducing costs. However, highly accurate analysis of NGS data is computationally intensive and creates a bottleneck in the overall sequencing workflow. The current gold standard in variant calling is the Genome Analysis Toolkit (GATK) 1 Best Practice Workflow pipeline using HaplotypeCaller, which is regarded to have the highest accuracy for both single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels). 2,3 However, its slow computation speed often makes adoption challenging. To address these challenges, the Sentieon DNA Software Package was developed to significantly decrease the analysis time and the computational resource requirements for variant detection without compromising accuracy. The result is a 20-to-50-fold increase in processing speed on the same hardware with results that are identical to the GATK pipeline, with differences within the numerical noise.”

The Sentieon Genomics Tools

A fast and accurate solution to variant calling from next-generation sequence data

“In the past six years, worldwide capacity for human genome sequencing has grown by more than five orders of magnitude, with costs falling by nearly two orders of magnitude over the same period [1], [2]. The rapid expansion in the production of next-generation sequence data and the use of these data in a wide range of new applications has created a need for improved computational tools for data processing. The Sentieon Genomics tools provide an optimized reimplementation of the most accurate pipelines for calling variants from next-generation sequence data, resulting in more than a 10-fold increase in processing speed while providing identical results to best practices pipelines. Here we demonstrate the consistency and improved performance of Sentieon’s tools relative to BWA, GATK, MuTect, and MuTect2 through analysis of publicly available human exome, low-coverage genome, and high-depth genome sequence data.”

If you’re interested in processing genomics data with high computing efficiency, fast turnaround time, exceptional accuracy and 100% consistency, request a free trial of Sentieon by filling out this form  or emailing us directly at!

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