Difference between revisions of "Spiral Genetics"
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{{Bioinformatics application | {{Bioinformatics application | ||
| − | |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. | + | |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. |
| − | + | |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 | |
| − | + | |bio method=Sequence alignment, File reformatting, Read mapping, | |
| − | |bio domain= | ||
| − | |bio method= | ||
|bio tech=Illumina | |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 | ||
| − | |input format=Fastq, Fastq.gz | + | |email address=info@spiralgenetics.com |
| − | |output format= | + | |input format=Fastq, Fastq.gz |
| − | |sw feature=Accurate, Fast | + | |output format=VCF 4.1 |
| + | |sw feature=Accurate, Fast, Cloud Computing, Read mapping, SNP calling, command line, large SV detection | ||
|language=C++, | |language=C++, | ||
|licence=Commercial, | |licence=Commercial, | ||
|os=Linux, Mac OS X, Windows | |os=Linux, Mac OS X, Windows | ||
}} | }} | ||
| − | + | Fast, scalable alignment and analysis at a price any lab can afford. | |
| − | + | ||
| − | < | + | <strong>Highlights</strong> |
| − | + | ; 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> | + | <strong>How does Anchored Assembly work?</strong> |
| − | + | ||
| − | + | 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. | |
| − | <strong> | + | |
| − | + | 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> | |
* Read Alignment (BWA, Bowtie and T-Map) | * Read Alignment (BWA, Bowtie and T-Map) | ||
* SNPs and Indels (SOAP and Maq) | * SNPs and Indels (SOAP and Maq) | ||
| Line 46: | Line 45: | ||
* Cloud and Cluster Versions | * Cloud and Cluster Versions | ||
* Ion Torrent Plugin to stream data directly to Spiral Cloud | * 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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