Overview
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, and SV calling is supported from short and long read data with award-winning accuracy through the use of platform-specific model files. UMI consensus generation, large-scale joint calling, CRISPR off-target detection, sample quality control and 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 2700 petabases of sequence. You can find out how our customers are using the Sentieon® tools in the citations page.
Featured Pipeline - DNAscope
Sentieon DNAscope provides improved accuracy due to improved active region detection, more powerful local assembly of reads, and incorporation of pre-trained machine learning models for both short reads and long reads sequencers.
Published preprint demonstrating world-class accuracy;
Whole-genome 30x fastq to VCF within 30 mins;
Supports short and structural variant calling;
Co-authored appnote demonstrating world-class accuracy;
Whole-genome 30x fastq to VCF within 30 mins;
Supports short and structural variant calling;
Co-authored preprint demonstrating world-class accuracy;
Award-winning pipeline for SNP/Indel/SV detection;
Processing speed 6x faster than DeepVariant;
Co-announced benchmarks demonstrating world-class accuracy;
Customized pipeline and models;
Calling variants from 30x WGS within 22 mins;
Published manuscript demonstrating highest accuracy;
Optimized model available;
Whole-genome 30x fastq to VCF within 30 mins;
Optimized pipeline for SNP/Inde/SV detection;
Higher accuracy than Clair3 and Sniffles2;
DNAscope for ONT Pipeline is 3-5x faster;
Feature Highlights
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.
Supported Applications
| Alignment | Sentieon® BWA, STAR, Minimap2: match open source result with ~2-4X speedup. |
| Germline SNV/INDEL Variant Calling | DNAseq®: PrecisionFDA award-winning software. Matches GATK v3.7-4.4, and without downsampling. Results up to 10x faster and 100% consistent every time. Read more. DNAscope: Machine learning enhanced filtering producing top variant calling accuracy. Supports both short and long reads from all mainstream sequencers. Read more. |
| Somatic SNV/INDEL Variant Calling | TNseq®: Matches MuTect, MuTect2 v3.7 - 4.2 without downsampling for higher accuracy and improved detections of low allelic fraction variants. Read more. TNscope®: Winner of ICGC-TCGA DREAM challenge. Improved accuracy, machine learning enhanced filtering. Supports high depth panel datasets. Read more. |
| Structural Variant Calling | Support short and long reads. 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. 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. |