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Spiral Genetics, Inc.

Seattle, Washington, US

Spiral Genetics provides a novel aligner/variant caller, Anchored Assembly, which can detect large structural variations using short read NGS data with unmatched precision.

Highlights:

• Unparalleled accuracy
Anchored Assembly accurately detects SNPs, indels, and structural variants ranging from 10bp to 100kbp.
• Use existing HiSeq data
Anchored Assembly uses data from HiSeq and MiSeq without special library prep. You can detect structural variants using your existing data.
• Low false positive rate
We optimize Anchored Assembly to ensure a very low false positive rate.
• High throughput
Reliably detect your variants at the rate that you produce data.

How Does Anchored Assembly Work?

Spiral’s Anchored Assembly uses direct, de novo read overlap assembly to accurately detect SNPs, indels, and structural variants.

Application of read overlap assembly to high-coverage whole genome data... Show more »

Spiral Genetics provides a novel aligner/variant caller, Anchored Assembly, which can detect large structural variations using short read NGS data with unmatched precision.

Highlights:

• Unparalleled accuracy
Anchored Assembly accurately detects SNPs, indels, and structural variants ranging from 10bp to 100kbp.
• Use existing HiSeq data
Anchored Assembly uses data from HiSeq and MiSeq without special library prep. You can detect structural variants using your existing data.
• Low false positive rate
We optimize Anchored Assembly to ensure a very low false positive rate.
• High throughput
Reliably detect your variants at the rate that you produce data.

How Does Anchored Assembly Work?

Spiral’s Anchored Assembly uses direct, de novo read overlap assembly to accurately detect SNPs, indels, and structural variants.

Application of read overlap assembly to high-coverage whole genome data is a challenge because of its computational demands. Anchored Assembly reduces this computational complexity by focusing analysis on non-reference sequence regions.

We map variant sequence regions to specific genome locations by “anchoring” the variant assembly to unique, non-repetitive sequence strings present in the reference genome. Assembly begins from these reference-anchored reads and traverses variant regions by constructing a read overlap graph. Because these anchors map to unique chromosomal coordinates on the reference, novel variants can be interpreted in the context of known genome features.

Accuracy of reads is critical to read overlap assembly. We use the A-star (A*) search algorithm together with a k-mer de Bruijn graph to correct reads without using a reference. This method leads to an approximate 100-fold reduction in the error rate of Illumina HiSeq reads.

System Specifications:

Anchored Assembly uses standard Illumina HiSeq reads that meet the requirements shown below. No special preparation is necessary.

• Type of Read: Single end reads, or Paired reads, or Mate-paired reads.
• Read Length: 100 bp or greater
• Coverage: 20x coverage minimum per chromosome set (e.g. 40x for a diploid genome).

Pricing for anchored assembly is dependent on the size and coverage of the dataset. For Analysis, please contact us for a quote at info@spiralgenetics.com

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DNA Sequencing Data Analysis
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Bioinformatics
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Spiral's Anchored Assembly uses direct de novo read overlap assembly to more accurately detect and characterize SNPs, indels, and structural variants.

Anchored Assembly provides an integrated method for both SNP and structural variant detection to produce specific results without process-specific biases. Anchored Assembly... Show more »

Spiral's Anchored Assembly uses direct de novo read overlap assembly to more accurately detect and characterize SNPs, indels, and structural variants.

Anchored Assembly provides an integrated method for both SNP and structural variant detection to produce specific results without process-specific biases. Anchored Assembly has greater sensitivity and is able to detect 30% more SVs than array or Sanger validated datasets. In addition, Anchored's unmatched precision produces results with a false discovery rate of 0.16% in SVs as compared to Pidel in simulated data.

Next-generation sequencing studies are expected to generate massive volumes (read: petabytes) of raw data. This volume will grow as the cost-per-genome continues to decrease. Whether you would prefer to run Anchored Assembly on the cloud or install on your existing computing cluster, we can offer you a flexible solution to complete large-scale analyses within a reasonable time frame.

If you have invested in private computing infrastructure, Spiral Cluster may be the best fit for you. Installing Anchored Assembly on your existing cluster is a scalable option to meet your organization’s specific cluster requirements and data restrictions. If you are interested in building a compute cluster specifically to run Anchored Assembly, contact us to discuss certified hardware.

Spiral Cloud offers a scalable alternative to investing resources to build your own infrastructure. Running Anchored Assembly on the cloud is simple to use with its command-line interface and accessible on any internet-enabled Windows, Mac, or Linux machine.

For information on data requirements for input and output data, please visit our Website:
http://www.spiralgenetics.com/products/data-requirements/

For pricing inquires, please contact one of our Bioinformaticians at info@spiralgenetics.com

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NGS data analysis
Next generation sequencing data analysis
Price on request

Spiral’s Anchored Assembly method uses direct de novo read overlap assembly to more accurately detect and characterize SNPs, indels, and structural variants. By using unmapped reads for de novo assembly, we accurately detect variants across a whole human genome with a low false positive rate. The tool is suitable for use with... Show more »

Spiral’s Anchored Assembly method uses direct de novo read overlap assembly to more accurately detect and characterize SNPs, indels, and structural variants. By using unmapped reads for de novo assembly, we accurately detect variants across a whole human genome with a low false positive rate. The tool is suitable for use with Illumina X, HiSeq, or MiSeq reads with at least 20x coverage per chromosome set (i.e. 40x coverage for diploid).

Anchored Assembly has greater sensitivity to structural variations and can detect 30% more SVs compared to array or Sanger validated datasets. In addition, Anchored Assembly offers unmatched precision with a lower false discovery rate than standard analysis pipelines like Pindel.

Next-generation sequencing studies are expected to generate massive volumes (read: petabytes) of raw data. This volume will grow as the cost-per-genome continues to decrease. Whether you would prefer to run Anchored Assembly on the cloud or install on your existing computing cluster, we can offer you a flexible solution to complete large-scale analyses within a reasonable time frame.

If you have invested in private computing infrastructure, Spiral Cluster may be the best fit for you. Installing Anchored Assembly on your existing cluster is a scalable option to meet your organization’s specific cluster requirements and data restrictions.
If you are interested in building a compute cluster specifically to run Anchored Assembly, contact us to discuss certified hardware.

Spiral Cloud offers a scalable alternative to investing resources to build your own infrastructure. Running Anchored Assembly on the cloud is simple to use with its command-line interface and accessible on any internet-enabled Windows, Mac, or Linux machine.

For Data Requirements on input and output data please visit Spiral Genetics Website:
http://www.spiralgenetics.com/products/data-requirements/

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