HiTea

HiTea identifies non-reference transposable element (TE) insertions genome-wide using Hi-C sequencing data to leverage chromatin interaction-derived read signals.

Key Features:

• Detection of Active Human Transposable Elements: HiTea is specifically tailored to identify insertions from three major classes of active human transposable elements: Alu (SINE), L1HS (LINE), and SVA.
• Utilization of Clipped and Split Hi-C Reads: HiTea leverages clipped and split Hi-C reads and discordant read pairs to detect TE insertions.
• Competitive Performance with WGS Data: Despite uneven genome coverage inherent to Hi-C, HiTea demonstrates competitive performance compared to callers based on whole-genome sequencing (WGS) data and provides complementary TE‑landscape characterization.

Scientific Applications:

• Genome Assembly and Structural Variation Identification: By utilizing long-range interaction information from Hi-C data, HiTea aids in generating chromosome-length genome assemblies and identifying large-scale structural variations.
• Supplementing WGS-Based Characterization: HiTea enhances the characterization of TE insertion landscapes when used alongside WGS-based methods.

Methodology:

HiTea processes Hi-C sequencing data using clipped and split read information, read coverage analysis, and discordant read-pair detection to identify non-reference TE insertions, including in regions with uneven genome coverage.