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. |
| + | See the white paper: | ||
http://www.spiralgenetics.com/science/resource-library/ | http://www.spiralgenetics.com/science/resource-library/ | ||
| + | |sw logo=Image for Spiral Genetics | ||
|bio domain=Alignment, DNA-Seq, Exome and Whole genome variant detection, De novo Assembly, Genomic Assembly, Mapping, Quality Control, Read alignment, Reference assembly, Resequencing, SNP discovery, Sequence analysis, Whole Genome Resequencing, | |bio domain=Alignment, DNA-Seq, Exome and Whole genome variant detection, De novo Assembly, Genomic Assembly, Mapping, Quality Control, Read alignment, Reference assembly, Resequencing, SNP discovery, Sequence analysis, Whole Genome Resequencing, | ||
|bio method=Alignment, De novo Assembly, Data compression, Genome Alignment, MapReduce | |bio method=Alignment, De novo Assembly, Data compression, Genome Alignment, MapReduce | ||
Revision as of 23:19, 11 July 2014
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Application data |
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| Created by | Spiral Genetics |
|---|---|
| Biological application domain(s) | Alignment, DNA-Seq, Exome and Whole genome variant detection, De novo Assembly, Genomic Assembly, Mapping, Quality Control, Read alignment, Reference assembly, Resequencing, SNP discovery, Sequence analysis, Whole Genome Resequencing |
| Principal bioinformatics method(s) | Alignment, De novo Assembly, Data compression, Genome Alignment, MapReduce |
| 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, 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. See the white paper: http://www.spiralgenetics.com/science/resource-library/ 200px|right
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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
Variant Detection is currently in beta. If you’d like to be part of our beta program, please contact us at info@spiralgenetics.com
Pricing starting at $12/GB (volume pricing)
Links
References
none specified
To add a reference for Spiral Genetics, enter the PubMed ID in the field below and click 'Add'.
Search for "Spiral Genetics" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
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