oliverhampton

Breakpoint-Primer-Design

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.

SVachra

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.

PEMapper

oliverhampton/PEMapper

oliverhampton/SVachra

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.

oliverhampton/Breakpoint-Primer-Design

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.