xTea

xTea identifies transposable element (TE) insertions in WES and WGS sequencing data from short-read and long-read platforms (Illumina, PacBio, Nanopore and hybrid combinations) to enable characterization and annotation of TE-mediated genomic variation.

Key Features:

• Comprehensive TE insertion identification: Detects TE insertions across genomic regions including highly repetitive and complex loci such as centromeres and telomeres.
• Support for short-read and long-read data: Processes both short-read and long-read sequencing datasets and hybrid combinations for integrated analysis.
• Enhanced performance on germline and somatic calls: Demonstrates improved discovery of germline and somatic TE insertions compared to short-read–only methods.
• Cataloging and assembly of polymorphic insertions: With long-read data enables creation of comprehensive catalogs, including full assembly and annotation of insertional sequences such as pseudogenes and endogenous retroviruses.
• Exploration of repetitive element reservoirs: Facilitates analysis revealing, for example, groups of full-length LINE-1 (L1) elements within centromeres as potential reservoirs of active TEs.

Scientific Applications:

• Genome structure and variation analysis: Characterizes how TE insertions alter genome architecture and contribute to structural variation.
• Gene regulation and disease studies: Investigates TE-mediated disruption of gene regulation and contributions to disease pathogenesis.
• Germline and somatic mutation discovery: Detects and differentiates germline versus somatic TE insertions in sequencing datasets.
• Polymorphic TE and retroelement cataloging: Generates annotated catalogs of polymorphic TEs and retroelements for population and functional studies.

Methodology:

Uses advanced algorithms to detect TE insertions by processing short-read and long-read sequencing inputs (WES/WGS from Illumina, PacBio, Nanopore or hybrid), integrates data across platforms, and performs assembly and annotation of insertional sequences.