TIGRA-SV is a program that conducts targeted local assembly of structural variants (SV) using the iterative graph routing assembly (TIGRA) algorithm (L. Chen, unpublished). It takes as input a list of putative SV calls and a set of bam files that contain reads mapped to a reference genome such as NCBI build36. For each SV call, it assembles the set of reads that were mapped or partially mapped to the region of interest (ROI) in the corresponding bam files. Instead of outputing a single consensus sequence, TIGRA-SV outputs all the alternative alleles in the ROI as long as they received sufficient sequence coverage (usually >= 2x). It is shown that TIGRA-SV is quite effective at improving the SV prediction accuracy in short reads analysis and can produce accurate breakpoint sequences that are valuable to understand the origin, mechanism and pathology underlying the SVs.
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