TranSurVeyor: an improved database-free algorithm for finding non-reference transpositions in high-throughput sequencing data.

ABSTRACT: Transpositions transfer DNA segments between different loci within a genome; in particular, when a transposition is found in a sample but not in a reference genome, it is called a non-reference transposition. They are important structural variations that have clinical impact. Transpositions can be called by analyzing second generation high-throughput sequencing datasets. Current methods follow either a database-based or a database-free approach. Database-based methods require a database of transposable elements. Some of them have good specificity; however this approach cannot detect novel transpositions, and it requires a good database of transposable elements, which is not yet available for many species. Database-free methods perform de novo calling of transpositions, but their accuracy i

SUBMITTER: Rajaby R 

PROVIDER: S-EPMC6237741 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature