SVachra (Structural Variation Assesment of CHRomosomal Aberrations) is an SV caller for Nextera mate pair sequencing consisting of both inward and outward facing read types. SVachra is a play on the word “chakra” describing the ability to call genomic SV by simultaneously evaluating inward and outward facing read pairs.
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Ruby scripts to generate breakpoint spanning primers for aberrant fusion PCR validation. These scripts will generate Primer3 input sequences across two distinct genome annotations (in .lff format) . Primer3 is executed, results parsed, and subjected to InsilicoPCR to ensure that no amplicon is produced when applied to the normal genome.