Difference between revisions of "Spiral Genetics"

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{{Bioinformatics application
 
{{Bioinformatics application
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|sw summary=Spiral Genetics provides alignment to reference, variant detection, variant filtering and annotation for any sized next generation sequencing dataset.  Using cloud computing, the Spiral Platform can produce results at ultra high speeds through a web browser interface.
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|sw summary=Spiral Genetics provides a novel aligner/variant caller, Anchored Assembly, which can detect large structural variations using short read NGS data with unmatched precision.
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|bio domain=Alignment, Comparative Genomics, DNA-Seq, Exome and Whole genome variant detection, Genomic Assembly, Integrated solution, Mapping, Quality Control, Read alignment, Reference assembly, Resequencing, SNP Annotation, SNP discovery, Sequence analysis, Sequencing, Targeted assembly, Targeted resequencing, Whole Genome Resequencing,
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|bio domain=DNA-Seq, Exome and whole genome variant detection, Genomic assembly, Quality control, Mapping, Sequence assembly, SNP detection, Sequence analysis, Whole genome resequencing, Statistical calculation
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|bio method=Alignment, Annotation, Assembly, Burrows-Wheeler, Data compression, Genome Alignment, Hadoop, MapReduce, Mapping, Trimming, SNP discovery,
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|bio method=Sequence alignment, File reformatting, Read mapping,  
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|bio tech=any,
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|bio tech=Illumina
 
|created by=Spiral Genetics
 
|created by=Spiral Genetics
 
|created at=http://www.spiralgenetics.com
 
|created at=http://www.spiralgenetics.com
 
|maintained=Yes
 
|maintained=Yes
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|input format=FASTA, FASTQ, Fasta.gz, Fastq.gz,
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|email address=info@spiralgenetics.com
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|output format=Tab-delimited file,
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|input format=Fastq, Fastq.gz
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|sw feature=Accurate, Fast, Gapped alignment, Ungapped alignment, Cloud Computing, Hadoop, Mapping, SNP annotation, SNP calling, command line, filter-based annotation,
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|output format=VCF 4.1
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|sw feature=Accurate, Fast, Cloud Computing, Read mapping, SNP calling, command line, large SV detection
 
|language=C++,
 
|language=C++,
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|licence=Commercial,  
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|licence=Commercial,
 
|os=Linux, Mac OS X, Windows
 
|os=Linux, Mac OS X, Windows
 
}}
 
}}
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<blockquote>"Spiral is a revolutionary sequence analysis software platform that puts the power of cloud computing at your fingertips.]
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Fast, scalable alignment and analysis at a price any lab can afford.
  
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Rapid improvements in next generation sequencing technology and decreases in cost have created an exponential amount of sequence data to be analyzed. With the massive influx of data, you need analysis software that is fast, user-friendly, and cost-effective. Spiral unlocks whole genome, exome, and targeted sequencing, with a solution that offers speed, simplicity, and savings."
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<strong>Highlights</strong>
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</blockquote>
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; Accurate : 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.
 +
 
 +
<strong>How does Anchored Assembly work?</strong>
 +
 
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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 sequences to specific genome locations by “anchoring”, or matching the ends of the assembled variant, to unique sequences present in the reference genome.  Assembly begins from these reference-anchored reads and traverses variant regions by constructing a read overlap graph.
 +
 
 +
<strong>Available via Cloud or Cluster</strong>
 +
 
 +
<strong>Features:</strong>
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* Read Alignment (BWA, Bowtie and T-Map)
 +
* SNPs and Indels (SOAP and Maq)
 +
* Assembly Based Variant Detection
 +
* Effect Prediction
 +
* Associated Gene and Pathways
 +
* Associated Phenotypes and Disease
 +
* KEGG, OMIM, LOVD and PharmGKB Links
 +
* Ensembl Browser Display
 +
* Upload/Download Common Data Formats
 +
* Cloud and Cluster Versions
 +
* Ion Torrent Plugin to stream data directly to Spiral Cloud
 +
 
 +
For more information please contact us at
 
{{Links}}
 
{{Links}}
 
{{References}}
 
{{References}}
 
{{Link box}}
 
{{Link box}}

Latest revision as of 00:14, 20 December 2015

Application data

Created by Spiral Genetics
Biological application domain(s) DNA-Seq, Exome and whole genome variant detection, Genomic assembly, Quality control, Mapping, Sequence assembly, SNP detection, Sequence analysis, Whole genome resequencing, Statistical calculation
Principal bioinformatics method(s) Sequence alignment, File reformatting, Read mapping
Technology Illumina
Created at http://www.spiralgenetics.com
Maintained? Yes
Input format(s) Fastq, Fastq.gz
Output format(s) VCF 4.1
Software features Accurate, Fast, Cloud Computing, Read mapping, SNP calling, command line, large SV detection
Programming language(s) C++
Licence Commercial
Operating system(s) Linux, Mac OS X, Windows
Contact: info@spiralgenetics.com

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

"Error: no local variable "counter" was set." is not a number.

Fast, scalable alignment and analysis at a price any lab can afford.

Highlights

Accurate 
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 sequences to specific genome locations by “anchoring”, or matching the ends of the assembled variant, to unique sequences present in the reference genome. Assembly begins from these reference-anchored reads and traverses variant regions by constructing a read overlap graph.

Available via Cloud or Cluster

Features:

  • Read Alignment (BWA, Bowtie and T-Map)
  • SNPs and Indels (SOAP and Maq)
  • Assembly Based Variant Detection
  • Effect Prediction
  • Associated Gene and Pathways
  • Associated Phenotypes and Disease
  • KEGG, OMIM, LOVD and PharmGKB Links
  • Ensembl Browser Display
  • Upload/Download Common Data Formats
  • Cloud and Cluster Versions
  • Ion Torrent Plugin to stream data directly to Spiral Cloud

For more information please contact us at

Links


References

none specified


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