GenomeSuite Analyzer

Human Genome
Structural Variant Caller

GenomeSuite Analyzer is a human genome structural variant (SV) caller for Nanopore long-read sequencing datasets. It accurately detects SV’s in germline, somatic and population-level sequencing data.

Discover Hidden Genetic Insights

Discover critical structural variants with our advanced algorithms. Detect complex genomic rearrangements with unparalleled accuracy, revealing crucial information about disease risks and inheritance patterns.

Accelerate Genetic Analysis Time

Our streamlined software processes whole genomes in hours, not days, without sacrificing precision. Rapidly identify insertions, deletions, inversions, and translocations to keep your projects on schedule and your discoveries flowing. Speed up your workflow for time critical diagnostics.

Easy Bioinformatics Pipeline Integration

With support for Nanopore POD5 and FAST5 file formats, you'll spend less time wrangling data and more time interpreting it. Trust in results backed by rigorous validation and join the growing community of researchers advancing the field of structural genomics.

About GenomeSuite Analyzer

  • High Sensitivity: Accurately detects complex SVs, including repeat-rich regions

  • Long-read analysis: Works with Oxford Nanopore sequencer long-read datasets

  • Precision: Capable of read-based phasing and accurate breakpoint detection

  • Automatic Filtering: Filters out false positive events automatically

  • Low-Coverage Data Compatibility: Operates effectively on low-coverage datasets, making it cost-efficient

  • Discovery of Novel Variants: Has uncovered thousands of novel variants in various genomic datasets

GenomeSuite Analyzer Detects Many SVs

Structural variant changes can significantly impact an organism's phenotype and health. By identifying a wide range of structural variants, GenomeSuite Analyzer provides a more complete picture of genetic diversity within populations, aid in diagnosing genetic disorders, and contribute to our understanding of evolutionary processes. This capability is critical in personalized medicine, where a thorough understanding of an individual's genetic makeup can inform treatment decisions and disease risk assessments.

  • Deletions

  • Duplications

  • Insertions

  • Inversions

  • Translocations

  • Copy Number Variants (CNVs)

  • Tandem Duplications

  • Segmental Duplications

  • Complex Rearrangements

  • Chromothripsis

  • Chromoplexy

  • Balanced Translocations

  • Unbalanced Translocations

  • Ring Chromosomes

  • Dicentric Chromosomes

  • Large Insertions (Transposable Elements)

  • Subtelomeric Rearrangements

  • Telomere Shortening

  • Telomere Elongation

  • Polymorphic Inversions

  • Microsatellite Expansions

  • Large Insertions (Transposable Elements)

  • Subtelomeric Rearrangements

  • Telomere Shortening

  • Telomere Elongation

  • Polymorphic Inversions

  • Microsatellite Expansions

  • Variable Number Tandem Repeats (VNTRs)

  • Heterochromatic Variations

  • Chromosomal Fusions

  • Chromosomal Fissions

  • Large-scale Structural Polymorphisms

  • Intra-chromosomal Translocations

  • Inter-chromosomal Translocations

  • Structural Variants involving Repetitive Elements

  • Chromosomal Duplication/Amplifications

  • Gene Fusions

  • Large Segmental Duplications

  • Mobile Element Insertions

  • Non-allelic Homologous Recombination (NAHR) Variants

  • Chromosomal Aneuploidy

  • Isochromosomes

  • Gene Conversion Events

Human Reference Genome

GenomeSuite Analyzer uses T2T-CHM13v2.0+Y as the reference genome for sequence alignments and structural variant calls.

T2T-CHM13v2.0+Y is the first complete, gapless assembly of the human genome. It is considered the gold standard for bioinformatic analysis of human genetic variation.

Analyzer Specs

Current Version Release Date
v.1.3.0 09/18/24
Input File Description
POD5 Nanopore POD5 file
FAST5 Nanopore FAST5 file
BAM BAM file
Output File Description
VCF VCF file

Hosted On

Service Type   Description
SeqCenter Managed Service   SeqCenter staff run Analyzer on your behalf. Our staff collaborates with your organization to run Analyzer in the cloud and deliver results.
     
Self Service   You or your organization run Analyzer directly using an AWS (Amazon Web Services) AMI (Amazon Machine Image). Using self service requires some AWS technical expertise in your organization.

FAQ

How do I use Analyzer?
Analyzer is available in Amazon Web Services (AWS) as an Amazon Machine Image (AMI).

What type of human genome data does it use?
Analyzer processes human whole genome sequencing datasets, human exome datasets and human gene panels.

What type of sequencing data does Analyzer use?
Analyzer processes raw data files in POD5 or FAST5 format from Oxford Nanopore sequencers.

Why does whole genome analysis take much longer to run than exome analysis?
Human whole genome sequencing datasets are ca. 64X larger than human exome datasets. Exomes only represent about 1% - 2% of the entire human genome. Thus, the time required for analysis of the human exome is a fraction of whole genome.

Why is Analyzer so fast?
Analyzer uses NVIDIA GPU’s in the Hopper (H100), Ampere (A100) and Volta (V100) architectures for high-performance structural variant calling. These GPU’s are the fastest processors available for human genome analysis.

How long does it take to run a sample?
The turnaround time varies depending on the type of required analysis (whole genome, exome, gene panel) and the desired turnaround time. Whole genome analysis with the fastest possible turnaround time takes about 2 hours. Exome analysis with normal turnaround time takes about 10 minutes.

What human reference genome does Analyzer use for variant calling?
Analyzer uses the T2T-CHM13v2.0+Y human reference genome from the T2T consortium. This is the current gold standard for reference genomes.

How are results delivered?
Analyzer generates a standard VCF file that shows all of the identified structural variants. VCF files can be used in a wide variety of applications for downstream analysis, including those for correlating SV’s with disease states and drug recommendations.

How much does it cost?
The cost varies depending on the type of sequencing performed (whole genome, exome, gene panel) and the desired turnaround time. Contact Us to receive a quote.

How can I get support?
We provide extensive support for Analyzer. We can help with running Analyzer, estimating turnaround times, estimating costs working with input datasets and output results. Send us a note at support@thesequencingcenter.com or fill in the Contact Us form.

Need documentation support?

Quickly access, configure and run GenomeSuite Analyzer.