Products - Sentieon

Sentieon® provides complete solutions for DNA/RNA data with software that is deployable on any generic CPU-based computing system. Our software improves upon the BWA, STAR and Minimap2 aligners with accelerated alignment speeds while producing identical output. Germline and somatic SNV, Indel, SV, and CNV calling is supported from short- and long-read data with award-winning accuracy through the use of sequencing platform-specific model files. UMI consensus, large-scale joint calling, CRISPR analysis, quality control and BAM preprocessing are included through modular software components. Our products have been extensively tested and validated by customers, and have processed millions of samples totaling over 3000 petabases of sequence. You can find out how our customers are using the Sentieon® tools in the citations page.

Accelerated BWA/GATK Compliant Pipelines

Concordant with BWA-MEM, STAR, Minimap2, Picard and GATK for drop-in replacement, and 10x faster.
Compute Cost Reduction on Generic Hardware

Being deployed local or online, process a 30x WGS dataset in <30 minutes, at <2 USD compute costs.
Sequencer Agnostic and Highly Accurate

Winner of multiple precisionFDA Challenges, supporting mainstream sequencers with top accuracy.

Published preprint demonstrating industry leading accuracy;

Whole-genome 30x fastq to VCF within 30 mins;

Supports short and structural variant calling;

Read more
Co-authored appnote demonstrating world-class accuracy;

Whole-genome 30x fastq to VCF within 30 mins;

Supports short and structural variant calling;

Read more
Co-authored preprint demonstrating world-class accuracy;

Award-winning pipeline for SNP/Indel/SV detection;

Processing speed 6x faster than DeepVariant;

Read more
Customized pipeline and models;

Pangenome pipeline reaches highest accuracy;

Calling variants from 30x WGS within 100 mins;

Read more
Published manuscript demonstrating highest accuracy;

Optimized model available;

Whole-genome 30x fastq to VCF within 30 mins;

Read more
Optimized pipeline for SNP/Inde/SV detection;

Higher accuracy than Clair3 and Sniffles2;

3-5x faster than opensource pipelines;

Read more
Co-authored appnote demonstrating top accuracy;

DNAscope joint calling with non-Salus datasets;

Supports WGS and WES;

Read more
Combines short- and long-read data sequenced from the same sample;

Novel integrated alignment and variant calling pipeline;

Output SNP/Indel/SV/CNV from a single pipeline;

Efficiently complete analysis in 90 minutes;

Read more


Pipelines	DNAscope (short reads)	DNAscope Pangenome	DNAscope LongRead	DNAscope Hybrid	DNAseq	TNscope (somatic)	TNseq (somatic)
Alignment	✔	✔	✔	✔	✔	✔	✔
SNP/Indel	✔	✔	✔	✔	✔	✔	✔
SV	✔	✔	✔	✔		✔
CNV	✔	✔		✔
Segdup Genes	✔	✔		✔
UMI Process						✔
Matching GATK					✔		✔

• DNAscope (short reads) - DNAscope pipeline conducts short reads alignment, germline variant calling for SNP, Indel, SV, CNV, and Segdup.
• DNAscope Pangenome - DNAscope Pangenome pipeline conducts short reads alignment to graph reference genome, germline variant calling for SNP, Indel, SV, CNV, and Segdup.
• DNAscope LongRead - DNAscope LongRead pipeline conducts long reads alignment, germline variant calling for SNP, Indel, and SV.
• DNAscope Hybrid - DNAscope Hybrid pipeline conducts short- and long-reads alignment, germline variant calling for SNP, Indel, SV, CNV, and Segdup.
• DNAseq - DNAseq pipeline conducts short reads alignment, germline variant calling for SNP and Indel, matching GATK result.
• TNscope - TNscope pipeline conducts short reads alignment, UMI processing, somatic variant calling for SNP, Indel, and SV.
• TNseq - TNseq pipeline conducts short reads alignment, somatic variant calling for SNP and Indel, matching GATK result.


Alignment	Sentieon® BWA, STAR, Minimap2: Align short reads, long reads, and RNA reads, match open source result with ~2-4X speedup. Pan-alignment: graph aware aligner.
Germline SNV/INDEL Variant Calling	DNAscope: Machine learning enhanced filtering producing top variant calling accuracy. Supports both short and long reads from all mainstream sequencers. The DNAscope Hybrid pipeline can process short and long reads in an integrated manner. DNAseq®: PrecisionFDA award-winning software. Matches GATK without downsampling. Results up to 10x faster and 100% consistent every time.
Somatic SNV/INDEL Variant Calling	TNseq®: Matches MuTect2 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 high depth panel datasets.
Structural Variant / CNV Calling	Support short and long reads input. Germline and somatic SV calling, Germline CNV calling.
UMI Dedup	Sentieon UMI-consensus: part of ctDNA processing pipeline, process and dedup UMI family into computed consensus reads.
Segdup Gene Caller	Suppor Segdup Gene families including CFH, CYP2A6, CYP2B6, CYP2D6, GBA, HBA, IKBKG, LPA, OTOA, PMS2, RCCX, RH, SBDS, STRC.
Joint Calling	Supports large-cohort joint calling of over 200,000 WGS samples directly from gVCF and without intermediate steps. Support gVCFs from different sequencing platforms.
RNA Variant Calling	Matches GATK RNAseq variant calling Best Practices and 10x faster. Support single cell analysis pipeline.
BAM Processing	Accelerated BAM utility tools including sort, dedup, re-align, BQSR. Dedup tool supports consensus-based deduplication with or without UMI, DNA or RNA datasets.
Quality Control	Variety of QC tools for BAM and FASTQ files, 20x faster than corresponding opensource tools.
Gene Editing Efficiency Analysis	Calling on/off-target gene editing events, calculate editing efficiency.

Genome Sequencing Service Providers
Molecular Diagnostic Companies
Pharmaceutical and Biotech Companies
Hospitals and Cancer Centers
Direct to Consumer Genomics Companies
Academic and Research Institutes

Overview

Accelerated BWA/GATK Compliant Pipelines

Compute Cost Reduction on Generic Hardware

Sequencer Agnostic and Highly Accurate

Featured Pipeline - DNAscope

The Sentieon Pipeline & Functions

The Sentieon Toolkit & Capabilities

Who We Serve

Genome Sequencing Service Providers

Molecular Diagnostic Companies

Pharmaceutical and Biotech Companies

Hospitals and Cancer Centers

Direct to Consumer Genomics Companies

Academic and Research Institutes