SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads.

ABSTRACT:

Background

Characterization of genomic structural variation (SV) is essential to expanding the research and clinical applications of genome sequencing. Reliance upon short DNA fragment paired end sequencing has yielded a wealth of single nucleotide variants and internal sequencing read insertions-deletions, at the cost of limited SV detection. Multi-kilobase DNA fragment mate pair sequencing has supplemented the void in SV detection, but introduced new analytic challenges requiring SV detection tools specifically designed for mate pair sequencing data. Here, we introduce SVachra - Structural Variation Assessment of CHRomosomal Aberrations, a breakpoint calling program that identifies large insertions-deletions, inversions, inter- and intra-chromosomal translocations utilizing both

SUBMITTER: Hampton OA 

PROVIDER: S-EPMC5629590 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature