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Spiral Genetics, Inc.

Seattle, Washington, US

POPULATION ANALYSIS
Spiral Genetics' BioGraph™ technology addresses the unique challenge of comparing large genomic datasets. The volume of raw read data and the need to reanalyze the data over time is computationally expensive. BioGraph converts read data into a highly efficient graph structure making it possible to quickly query as genomic references or variant detection algorithms change.

STRUCTURAL VARIANT ANALYSIS
Structural variants are becoming increasingly important as research expands to populations that are not well represented by the "reference genome". Popular open-source variant callers have false discovery rates (FDRs) as high as 40% making it difficult to compare variants. BioGraph Assembly harmonizes data from different callers without requiring reanalysis and has a 3% FDR.

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Bioinformatics
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Population Analysis
The Spiral Genetics BioGraph Toolkit is an advanced, indexed, graph-based suite of products for genomic data management, analysis, and discovery. The BioGraph Analysis Format is a method of storing NGS read data using a whole read overlap assembly that has been indexed with advanced... Show more »

Population Analysis
The Spiral Genetics BioGraph Toolkit is an advanced, indexed, graph-based suite of products for genomic data management, analysis, and discovery. The BioGraph Analysis Format is a method of storing NGS read data using a whole read overlap assembly that has been indexed with advanced technology.

Incorporates all read data, across hundreds of individuals using a read overlap graph.
This read overlap graph can be queried at the rate of over 100,000 queries a second on just 8 cores.
With the API, different tools can be scripted to identify anything from gene fusions, and de novo and structural variants, to the allele frequency of SNPs across 1000 individuals.
The read data for multiple individuals can be stored in less than 3GB per individual.
This format allows for very rapid query of all the reads, not just those aligned to the reference. It is a graph representation, making it possible to directly compare between samples, even for areas that have not been mapped to the reference.

Essentially, the approach includes a method of preprocessing input files and putting them into a graph format, which both captures the sequence reads in their entirety and makes them much easier to search. Unlike the standard approach for detecting variants, which aligns input sequences to a reference, looks for mismatches, and then generates a list of variants leaving out information about the reads from which the variant calls were made, in BioGraph reads are indexed in stacked graphs, which makes it easy for users to search for variations by following paths through the graphs.

Spiral Genetics® and BioGraph™ products are trademarks of Spiral Genetics, Inc.

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Bioinformatics Data Analysis
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Structural Variant Analysis
BioGraph Assembly is a structural variant caller built on top of Spiral's BioGraph Format.

One of the biggest challenges in large-scale sequencing is the ability to detect complex changes in the genome. These complex structural changes are important for understanding neurological disorders,... Show more »

Structural Variant Analysis
BioGraph Assembly is a structural variant caller built on top of Spiral's BioGraph Format.

One of the biggest challenges in large-scale sequencing is the ability to detect complex changes in the genome. These complex structural changes are important for understanding neurological disorders, cardiological conditions, rare childhood disorders, and investigating changes across individuals. Today's tools often miss many structural variations or are limited to one type, such as deletions. In addition, most tools have high false discovery rates, requiring considerable time sifting through structural variant calls to differentiate between real variants and false positives.

BioGraph Assembly offers a strong combination of high sensitivity and low false discovery rate with accurate breakpoints. Leveraging high thoughput short-read NGS data to detect comprehensive variation including large indels (20 bp), larger structural variation events like segmental duplication (1kb - 20kb+), and full insertion sequence recovery (100 - 5kb+). Using a method that assembles reads first and maps back to the reference after, we dramatically reduce reference bias and can accurately detect changes often not detected by other methods. Specifically, the method searches for reads that have not aligned to the reference and then follows the read overlap assembly in both directions until over 70% of the reads match the reference. This is reported as a variant. Utilizing the BioGraph Format, this search for structural variants can be completed in approximately 4 hours.

Spiral Genetics® and BioGraph™ products are trademarks of Spiral Genetics, Inc.

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