• Identical mathematics as Broad Institute’s BWA-GATK Best Practice Workflow, but 10X faster FASTQ-to-VCF, 20X faster BAM-to-VCF, measured in core-hours
• No run-to-run difference, no down-sampling in high coverage regions
• Large cohort (>200K samples) Joint-calling without intermediate file merging
• Centers for Common Disease Genomics (CCDG) functionally equivalent
• Pure software solution running on any generic-CPU-based system
• Winner of precisionFDA Consistency Challenge
• Winner of precisionFDA Truth Challenge
• Winner of precisionFDA Hidden-Treasure Warm-Up Challenge
• FASTQ-to-VCF performance on a 64-core machine in the Google Cloud:
  • 30x Genome, NA12878 (HG001), in 2 hours (140 core-hours)

Sentieon® DNAseq® implements the same mathematics used in the Broad Institute’s BWA-GATK HaplotypeCaller 3.3-4.1 Best Practices Workflow pipeline, but with more efficient computing algorithms and an enterprise-strength software implementation. The improved computing algorithms enable Sentieon® DNAseq® users to complete a 30x WGS from FASTQ-to-VCF for less than $1 in cloud computing costs. Compared to the BWA-GATK, Sentieon® DNAseq® is 10X more efficient in core-hours for processing from FASTQ-to-VCF, while using the same generic-CPU-based system with no special hardware requirements. For aligned-BAM-to-VCF processing, Sentieon® DNAseq® is 20X faster than GATK. The software is also able to perform joint calling on over 200K samples simultaneously without intermediate file merging.

Through the improved computing algorithms and a rigorous multithreaded software implementation, Sentieon® DNAseq® has no run-to-run differences, because Sentieon® DNAseq® does not down-sample in high coverage regions and has no thread-dependency. Such consistency is critically important for clinical applications, and for applications that require high sequencing coverage.

These improvements have enabled Sentieon® DNAseq® to win the precisionFDA Consistency, Truth, and Hidden Treasure Warm-up challenges. As demonstrated in the precisionFDA challenges, Sentieon® DNAseq® achieves accuracy higher than the original BWA-GATK  pipeline by eliminating the randomness and noise from the software implementation, while using the same mathematics.

Sentieon® DNAseq® is an easily scalable, easily deployable, easily upgradable, software-only solution. It increases the productivity of existing computing infrastructure by over 10X, or reduces cloud computing cost more than 10X through improved efficiency. The command line interface is similar to the GATK pipeline with a straightforward mapping between Sentieon® and BWA-GATK commands, enabling flexible application pipelines composed of individual modules corresponding to GATK pipeline stages, including pipelines that meet the Centers for Common Disease Genetics (CCDG)’s functional equivalence specification.

Sentieon® maintains DNAseq® and will continue to match new BWA-GATK releases. On top of this baseline, Sentieon® works with customers to develop new features that further improve accuracy and add functionality.

For a 30X whole genome sequence, Sentieon® DNAseq® completes the full pipeline, FASTQ-to-VCF, in about 2 hours, on a single 64-core server. When turnaround time is critical, Sentieon® DNAseq® is also distributed-processing ready, allowing reduction of FASTQ-to-VCF time to less than half an hour using multiple servers.

Sentieon® DNAseq® was built on the solid foundation of the most rigorous and most extensively tested and validated mathematical models used in the Broad Institute’s Best Practices Workflow, but with more efficient computing algorithms and an enterprise-strength software implementation.

Key features:

• Enhanced variant calling sensitivity and accuracy though improved local assembly and machine learning model
• Supports HiFi long reads with award-winning accuracy and speed
• Fast and efficient, speed similar to DNAseq
• No run-to-run difference, no down-sampling in high coverage regions
• Winner of precisionFDA Truth Challenge
• Winner of precisionFDA Truth Challenge V2

Sentieon® DNAscope builds upon and improves the mathematical models used in DNAseq®. Sentieon® DNAscope improves local assembly for complex variants detection for both short reads and long reads. It also includes a machine-learning/AI module to further improve accuracy. Sentieon® DNAscope achieves best-in-class accuracy for all sequencing platforms with similar runtime as DNAseq®.

Sentieon® DNAscope is inherently multi-threaded and distributed-processing ready.

Key features: ​

• Identical mathematics as Broad Institute’s MuTect and MuTect2, but 10X faster FASTQ-to-VCF while never downsampling
• No run-to-run difference, no down-sampling in high coverage regions
• ​Pure software solution running on any generic-CPU-based systems

Sentieon® TNseq® is a paired tumor-normal or tumor-only somatic variant detection suite with algorithms matching MuTect and MuTect2. Sentieon® TNseq® implements the same mathematics used in the Broad Institute’s tools with efficient computing algorithms and an enterprise-strength software implementation to achieve performance improvements.

Sentieon® TNseq® is over 10X faster in core-hours, has no run-to-run difference, does not down-sample in high coverage regions, and is more robust. In addition to improved somatic variant calling from WGS or WES samples, Sentieon® TNseq® specifically enables high-coverage somatic variant calling applications such as liquid biopsies since Sentieon® TNseq® can process regions with coverage depths over 100k+ without down-sampling.

By design, Sentieon® TNseq® is inherently multi-threaded and is distributed-processing ready.