TEfinder

TEfinder identifies novel transposable element (TE) insertions from paired-end next-generation sequencing data to characterize genome dynamics and TE-mediated genetic variation.

Key Features:

• Discordant read analysis: Leverages discordant reads from paired-end sequencing to detect new TE insertion events.
• Minimal software dependencies: Requires BEDTools, SAMtools, and Picard.
• Input requirements: Operates from four inputs: a list of TEs present in the reference genome, binary paired-end alignment files, a reference genome index, and TE names.
• Broad applicability: Designed to function without species-specific input formats or extensive prior knowledge of target organisms.
• Validation: Demonstrated accurate detection in studies of evolving populations of Fusarium oxysporum, including short-term adaptation experiments.

Scientific Applications:

• Genome dynamics and evolution: Detection of novel TE insertions to study TE-driven genome rearrangements and evolutionary processes.
• Genomic instability and gene regulation: Identification of insertion events that may contribute to genomic instability or alter gene expression.
• Experimental evolution and population genomics: Tracking TE insertion polymorphisms in evolving populations and adaptation studies (e.g., Fusarium oxysporum).

Methodology:

Identifies insertions by analyzing discordant paired-end reads from next-generation sequencing alignments using SAMtools, BEDTools, and Picard with inputs: reference TE list, binary paired-end alignment files, reference genome index, and TE names.