Benchmarking computational tools for polymorphic transposable element detection.

ABSTRACT: Transposable elements (TEs) are an important source of human genetic variation with demonstrable effects on phenotype. Recently, a number of computational methods for the detection of polymorphic TE (polyTE) insertion sites from next-generation sequence data have been developed. The use of such tools will become increasingly important as the pace of human genome sequencing accelerates. For this report, we performed a comparative benchmarking and validation analysis of polyTE detection tools in an effort to inform their selection and use by the TE research community. We analyzed a core set of seven tools with respect to ease of use and accessibility, polyTE detection performance and runtime parameters. An experimentally validated set of 893 human polyTE insertions was used for this purpose,

SUBMITTER: Rishishwar L 

PROVIDER: S-EPMC5808724 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature