SENTIEON®

A highly-optimized algorithms for bioinformatics applications

Sentieon®

Feature Highlights

Use Cases

SENTIEON® Analysis Pipelines & Tools

Product Key Features

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Sentieon®

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

Sentieon® has been extensively tested and validated by customers, and have processed millions of samples totaling over 900 petabases of DNA. You could find out how our customers are using Sentieon® tools in the citations page.

Feature Highlights

Accelerated BWA-MEM and GATK compliant pipelines

Concordant with BWA-MEM, STAR, Minimap2, Picard and GATK3.3-4.1 for drop-in replacement of whichever flavor of “Broad Institute Best Practices Pipelines" you use

Rapid Turnaround Time and Cost Reduction

Process a 30x WGS from fastq-to-VCF in <30 minutes with distributed computing; or in <2 hours on a single server. 10x reduced computing costs, with identical results to BWA/GATK

100% Consistency

No down sampling, no thread dependency, and no run-to-run differences. Sentieon® tools won top overall performance and highest reproducibility awards in the PrecisionFDA Consistency Challenge

Easy Deployment

Software-only solution runs on any generic CPU based computing system; easy to deploy on-premise or in the cloud

Award Winning Accuracy

Winner of the precisionFDA Truth Challenge, PrecisionFDA Hidden Treasure Warm-Up Challenge, PrecisionFDA NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge, and the ICGC-TCGA DREAM Somatic Mutation Calling Challenge

Enterprise Support

Dedicated customer support by our expert scientists and engineers

Use Cases

Population Sequencing

Cost-effective whole genome and exome sequencing of large cohorts; joint calling of more than 200,000 WGS samples

Genetic Disease

Clinical whole genome, exome, and panel sequencing

Tumor Sequencing

Accurately identify variants from fresh, frozen, and FFPE biopsies or blood samples

Agrigenomics

Analyze complex and polyploid plant and animal genomes

Sentieon® Analysis Pipelines & Tools

Alignment Sentieon® BWA, STAR, Minimap2: identical match open source result with >2X speedup.
Germline SNV/INDEL Variant Calling

DNAseq®: PrecisionFDA award-winning software. Matches GATK 3.3-4.1, and without downsampling. Results up to 10x faster and 100% consistent every time.

DNAscope: Improved accuracy and genome characterization. Machine learning enhanced filtering producing top variant calling accuracy. Supports both short reads and PacBio HiFi long reads.
Somatic SNV/INDEL Variant Calling

TNseq®: Matches MuTect, MuTect2 v3.8 - 4.1 without downsampling for higher accuracy and improved detections of low allelic fraction variants.

TNscope®: Winner of ICGC-TCGA DREAM challenge. Improved accuracy, machine learning enhanced filtering. Supports molecular barcodes and unique molecular identifies.
Structural Variant Calling Germline and somatic SV calling, including translocations, inversions, duplications and large INDELs.
Joint Calling Supports large-cohort joint calling of over 200,000 WGS samples directly from gVCF and without intermediate steps.
BCL-FASTQ Tool Sentieon®'s external library accelerates BCL to FASTQ conversion by 1.5 - 2x.
RNA Variant Calling Matches GATK RNAseq variant calling Best Practices.

Product Key Features

Sentieon® DNAseq®
  • Identical mathematics as Broad Institute’s BWA-GATK Best Practice Workflow, 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
  • >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
Sentieon® DNAscope®
  • Enhanced variant calling sensitivity and accuracy though improved local assembly and machine learning model
  • New pipeline for HiFi long-read 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
Sentieon® TNseq®
  • Identical mathematics as Broad Institute’s Mutect and MuTect2, 10X faster FASTQ-to-VCF, measured in core-hours
  • No run-to-run difference, no down-sampling in high coverage regions
  • Pure software solution running on any generic-CPU-based system
Sentieon® TNscope®
  • Complete tumor-normal somatic variant detection suite, calling SNV, INDEL, and SV
  • No run-to-run difference, no down-sampling in high coverage regions
  • Pure software solution running on any generic-CPU-based system
  • Leads ICGC-TCGA DREAM Mutation Calling Challenge

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Sentieon® DNAseq®, for consistent and confident germline variant detection

Key features:

  • 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.

Sentieon® DNAscope, for accurate comprehensive germline variant detection

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.

Sentieon® TNseq®, for consistent and confident somatic variant detection

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.

Sentieon® TNscope®, for accurate comprehensive tumor characterization

Key features:

Sentieon® TNscope® builds upon and improves the mathematical models used in MuTect and MuTect2. Employing sophisticated signal processing techniques to accumulate signal while canceling noise, TNscope® enhances signal-to-noise ratio in variant detection, achieving higher sensitivity and specificity than comparable tools. All categories of variants are detected and characterized simultaneously, including SNV, INDEL, and structure variants eliminating the need to run multiple variant calling tools.

Sentieon® participated in the ICGC-TCGA organized DREAM Challenge benchmarking tumor-normal somatic variant calling accuracy, using the engineering version of TNscope®, and is leading with a solid margin in all 3 categories: SNV, INDEL, and SV. On the final leaderboard, Sentieon® achieved an F-score of 98.57% in SNV, 98.14% in INDEL, and 100% in SV.

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

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