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Similar a Omixon accurate variant detection slideshare version 2011 aug 17
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Omixon accurate variant detection slideshare version 2011 aug 17
- 1. Finding Novel Variants with Omixon Variant Toolkit Attila Berces, PhD CEO, Omixon
- 5. Late breaking development Omixon Read Mapper for Illumina, Ion Torrent and Roche
- 6. Omixon read mapper Scientific advances Sensitive handling of indels, especially tandem repeats Match/mismatch w/ local base composition Variable indexing density Letter space (Illumina, SOLiD5500, Roche, Ion Torrent) homopolymer error correction
- 7. Omixon read mapper User benefits Identify variants with more confidence higher coverage Identify difficult-to-find variants Save on consumables lower coverage Accurate read mapping at fast computational speed
- 8. Re-mapping validation Synthetic, 51 bpIllumina reads, experimental QVs
- 9. Sensitive handling of short repeats
- 10. Homo/hetero zygos double substitution
- 11. Four times exon coverage [0-96] BWA [0-432] Omixon
- 12. Higherexomecoverage [0-10] BWA [0-24] Omixon
- 13. Identify more valid variants BWA Omixon
- 14. Find homopolymerindels BWA Omixon
- 15. Why focus on variant analysis accuracy?
- 17. With scalable throughput and up to 99.99% accuracy, the SOLiD™ System enables you ……
- 19. Illumina sequencing systems, powered by TruSeq technology, deliver the most accurate data across a broad range of applications.
- 20. What is limiting the accuracy of variant analysis?
- 21. DNP example 100 % accurate synthetic SOLiD v.4 reads reproducing naturally occurring DNPs
- 22. Found DNPs Bioscope: bioscope-v1.3-rBS131_55029_20101119113500; BFAST 0.6.4f (2011-03-11); parameters: Clark MJ, Homer N, O'Connor BD, Chen Z, Eskin A, et al. PLoS Genet 6(1) SHRiMP 2.1.1b ( February 8, 2011) parameters: gmapper-cs -L database reads.csfasta -V -w 150% -n 1 -r 50% -v 55% -l 40% -Z -h 60% -a -1 (mapping in overly sensitive mode)
- 23. BFAST SHRiMP
- 24. … and with real data
- 25. Omixon Omixon Bioscope BFAST SHRiMP
- 26. Omixon Omixon Bioscope BFAST SHRiMP
- 27. Omixon Bioscope BFAST SHRiMP
- 28. Omixon Bioscope BFAST SHRiMP
- 29. Omixon Bioscope BFAST SHRiMP
- 30. Omixon Bioscope BFAST SHRiMP
- 31. Omixon Bioscope BFAST SHRiMP
- 32. Omixon Bioscope BFAST SHRiMP
- 33. First conclusion Read accuracy is not the limiting factor in accurate variant analysis
- 35. Visual inspection of short reads and variant calls
- 36. Sanger validation of inferred variants Omixon Omixon Omixon Omixon Omixon
- 37. Sanger validation of inferred variants Omixon Omixon Omixon Omixon Omixon
- 38. Second conclusion As variant density increases the performance of most tools go down
- 39. What types are the variants were only found by Omixon? DNPs TNPs Small indels, especially next to SNPs 9-12 bpindels Homopolymerindels Homopolymerindel and SNP together Indels in palindromes Variants within GA repeats Pairwise substitution in TATA box
- 41. Omixon Bioscope BFAST SHRiMP
- 42. Omixon Bioscope BFAST SHRiMP
- 43. Omixon Bioscope BFAST SHRiMP
- 44. Omixon Bioscope BFAST SHRiMP
- 45. Omixon Bioscope BFAST SHRiMP
- 46. Omixon Bioscope BFAST SHRiMP
- 47. Omixon Bioscope BFAST SHRiMP
- 48. Omixon Bioscope BFAST SHRiMP
- 49. Omixon Bioscope BFAST SHRiMP
- 50. Omixon Bioscope BFAST SHRiMP
- 51. Omixon Bioscope BFAST SHRiMP
- 52. Omixon Bioscope BFAST SHRiMP
- 53. Benefits of the Omixon plug-in for CLC bio workbench/server
- 54. Benefits of CLC bio plug-in Omixon CLC bio
- 55. Benefits of CLC bio plug-in Omixon CLC bio
- 56. Benefits of CLC bio plug-in Omixon CLC bio
- 57. Benefits of CLC bio plug-in Omixon CLC bio
- 58. Benefits of CLC bio plug-in Omixon CLC bio
- 60. The sensitivity specificity challenge
- 61. How is Omixon different?
- 62. Sequencer-specific algorithms SOLiD Illumina SOLiD 5500 Application-specific algorithms Exome-sequencing RNA-seq No sensitivity vs.specificitytrade-off Alignment based on DNA mutation model
- 65. Please view our poster.
- 66. No Smith-Waterman No artifacts to correct downstream Quality values used in alignment Quality recalibration is the result not the input of the process
- 67. Our SOLiD Alignment Tools Csuros, Juhos, Berces "Fast Mapping and Precise Alignment of AB SOLiD Color Reads to Reference DNA" Springer Lecture Notes in Bioinformatics6293:176-188, 2010.
- 73. Conclusions There is no perfect method today for variant analysis but significant differences exist in accuracy OmixonVariant Toolkit provides highly sensitive and accurate analysis
Notas del editor
- (double, triple substitutions, indels next to SNPs,10-30 bpindels, homopolymerindels, indels in palindromes, variants within GA repeats or TATA box)