This presentation describes some of our results in genomic variant detection. Using Omixon software we find variants not found by other software. We introduce a new short read mapping for Illumina, Ion Torrent and 454 for highly sensitive mapping and alignment especially for repeats. This is an excellent way to correct for homopolymer errors in 454 and Ion Torrent data. For a free download visit http://www.omixon.com/omixon/abouttoolkit2.htm .
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
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
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
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
Notes de l'éditeur
(double, triple substitutions, indels next to SNPs,10-30 bpindels, homopolymerindels, indels in palindromes, variants within GA repeats or TATA box)