• What is Sentieon?

Sentieon develops high-performance bioinformatics software for short-read and long-read sequencing (NGS) data analysis. We support all major sequencing platforms, including Illumina, Element Bio, Ultima Genomics, MGI, Genemind, Pacific Biosciences (PacBio), and Oxford Nanopore instruments.

• What applications does Sentieon support

The Sentieon software supports the following applications:

• Short-read germline or somatic variant calling with whole-genome, whole-exome, or panel (amplicon or target-capture) library preparations with DNA or RNA inputs.
• Long-read alignment and germline variant calling.
• Structural variant calling from short-read or long-read data.
• Molecular barcode (UMI) handling including consensus read generation and UMI-aware duplicate marking.
• Somatic variant calling from cell-free or circulating tumor DNA (cfDNA and ctDNA).
• Cohort joint calling – gVCF to multi-sample VCF processing.
• Special handling of clinically-relevant genes inside of segmental duplications (SMN1, HBA, GBA, PMS2, etc.). Read more;
• x star-allele calling.
• Preprocessing and comprehensive metrics collection from aligned sequencing reads.
• Mitochondrial variant calling.
• Short-tandem repeat (STR) expansions.

The Sentieon software is a flexible suite of tools for processing next-generation sequence data and can be adapted to support genome analysis and other applications not listed here.

• Does Sentieon require specialized hardware?

No, Sentieon does not require specialized hardware. Our bioinformatics software runs on standard x86 or ARM servers and cloud instances. We achieve acceleration purely through algorithmic optimization and software engineering - no GPUs or FPGAs are required.

• How does Sentieon software achieve its acceleration and efficiency?

Sentieon bioinformatics software achieves its acceleration and efficiency by developing improved algorithms which are used to speed the processing of genomics data. These algorithmic improvements are realized through a highly optimized and efficient software implementation. The result: orders-of-magnitude faster runtimes with 100% consistent results and very low compute costs.

• Why is Sentieon 100% consistent?

Sentieon is 100% consistent because our deterministic algorithms eliminate run-to-run variation common in stochastic or multi-threaded software. The software process all of the reads in the sample to enable consistency and high accuracy.

• What reference genomes does Sentieon support?

The Sentieon software can be used with reference genomes from any organism in FASTA format. CRAM format and CSI index are also supported for reference genome has contigs larger than 512Mb. The Sentieon software can also be used with pangenome references, including those produced by the Human Pangenome Reference Consortium or custom pangenomes.

• How accurate is Sentieon?

Sentieon has won multiple precisionFDA awards for accuracy and supports all major sequencing platforms. Sentieon consistently achieves accuracies above 0.999 for SNVs, and 0.997 for indels as measured by F1-score with short-read WGS samples.  The DNAscope Hybrid pipeline (with Pacbio Hifi at 10x and Illumina at 30x) further improves variant calling to fewer than 6,000 total errors.

• What types of variants are identified by the Sentieon short-read WGS pipeline

Sentieon strives to help you comprehensively characterize your samples. Sentieon’s short-read WGS pipeline can identify single-nucleotide variants (SNVs); small insertions and deletions (indels); structural variation including large insertions, deletions, translocations and copy-number variants (CNVs). Short Tandem Repeats and Mitochondrial variants are also called.

Sentieon recently added support for clinically relevant genes inside of segmental duplications including SNVs, indels, and structural variation (including gene conversion events).

• Has Sentieon been used in clinical pipelines?

Yes. Sentieon is deployed in CAP/CLIA and ISO-certified environments, including top reference labs, hospitals, and national research programs worldwide.

• How do free trials work?

Sentieon free trials provide users full access to the software package, with full customer support to ensure that your trial is successful. We have a flexible and generous free trial policy so you can be confident in the performance of the software before buying a license.

• How does time-based licensing work?

Sentieon offers annual time-based licenses for a flat fee that are priced on a rough estimate of usage. The license provides access to all the software’s capabilities, so you can use as much as you need, for whatever applications you need.

• Is support included?

Yes. All commercial licenses include technical support and updates for the duration of the license term.

• Can I use the same license on multiple machines?

Yes. Our license server model allows concurrent use across multiple nodes or clusters. You can compute wherever you have your data, locally or in any cloud.

• Do you offer academic pricing?

We offer an initial free tier for qualified academic institutions as well as paid licenses with academic pricing. Contact us to learn more.

• What platforms does Sentieon support?

Sentieon runs on Linux (CentOS, Debian, Amazon Linux, RHEL, and derivatives). We support x86 CPUs from Intel and AMD, as well as ARM64 architectures.

• Can I use Sentieon on the cloud?

Yes. Sentieon can be used on all major cloud providers including AWS, Azure, Google Cloud, and others. The Sentieon software can also be used in hybrid computing environments. The software is available through major genomics service providers such as DNAnexus, Golden Helix, and Amazon HealthOmics.

• Is containerization supported?

Yes. The Sentieon software is distributed as a self-contained software package with binary executables and libraries. The software can be incorporated into Docker or Singularity images for easy integration into existing pipelines and workflow systems.

• Can Sentieon run in an air-gapped system?

Yes. Sentieon can run on servers inside air-gapped environments using a license server connected to a USB dongle. Contact us to learn more.

• What’s the best place to start?

Visit free trial page to request an evaluation license. You’ll receive binaries, setup instructions, and example pipelines.

• Are there example datasets or tutorials?

Yes. Our documentation includes example commands, input/output examples, and reference data links to help you get started quickly. For most applications, the Sentieon support team can provide links to publicly accessible data that can be used to test the Sentieon software.

• What are best practices for WGS analysis with Sentieon?

Use our pre-configured pipelines for WGS or WES analysis of Illumina, Element, Pacbio, ONT, Ultima, or MGI data.

• How do I benchmark Sentieon pipelines?

Sentieon pipelines can be benchmarked using publicly available benchmark datasets from the Genome in a Bottle project, or commercially available control or reference materials. VCFs produced by the Sentieon pipelines can be benchmarked using standard evaluation tools such as hap.py or som.py. Runtimes of the Sentieon pipeline can be accessed from the pipeline job log.

• Who uses Sentieon?

Sentieon is used by leading research institutions, clinical diagnostic and biotech companies, and hospitals worldwide. Sentieon users from the Mayo Clinic noted,  “Not only are we pretty happy, Sentieon is hands down without comparison the best vendor we work with, bar none”.

• Can I collaborate with Sentieon?

Absolutely. We work with partners across research, clinical, and commercial domains to accelerate innovation in bioinformatics. If you’re developing new analysis tools or benchmarking workflows, we would love to collaborate.

• Where can I access documentation and user guides?

Documentation and tutorials are available at https://support.sentieon.com/docs/ and https://github.com/Sentieon.

• How do I contact support?

Email us at support@sentieon.com.

• Do you offer training or workshops?

We provide private onboarding sessions, benchmarking guidance, and optimization workshops for teams.

• How can I request new features?

We welcome feature requests from our user community. Contact us directly or through your support representative.