Multi-way Analysis
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Multiple TechnologiesCombine and intersect results from complementary algorithm and platform technologies |
Multiple GenomesInfer likely mutations from inheritance states in families or matched tumor / normal samples |
Novel PipelinesCombine diverse investigative functions into uniquely adapted analysis pipelines |
Multi-platform SNPCombining reads from different sequence technologies delivers higher variant call accuracy. The RTG snp command can apply platform-specific base quality information from both Illumina and Complete Genomics sequencing platforms to adjust variant call scoring. In a test with NA19240 reads, plotting true positive vs false positive variant calls at progressively higher posterior scores shows variant calls with the combined CG + Illumina read data to be more accurate than with either CG or Illumina data alone. |
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SNP IntersectionsDifferent analytical algorithms with unique and complementary methods produce results that overlap with each other. In the intersections, one has higher confidence in the reported variants. In the differences, one observes novel results that extend the value of an existing experiment. When applied to data from the 1000 Genomes Project, RTG variant pipeline functions in combination with BWA/GATK found evidence of 78.3% overlap while identifying 16% more novel variants. |
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Novel PipelinesThe mapping algorithm underlying RTG map has unique qualities that support innovative pipeline development. These include use of a compressed memory efficient data structure based on k-mers, and on demand indexing of reads. These qualities enabled development of a streamlined metagenomics analysis pipeline for use on Illumina sequence data from the Human Microbiome Project. |
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