DeviaTE

DeviaTE analyzes assembly-free Illumina or Sanger sequencing reads to quantify transposable element (TE) abundance and visualize TE coverage and sequence variation relative to single-copy genes.

Key Features:

• Assembly-free abundance estimation: Provides unbiased estimates of TE composition from Illumina or Sanger reads by contrasting TE coverage with single-copy genes across one or more samples.
• Visualization and tabular output: Generates tabular data and visual representations of coverage, sequence divergence, segregating SNPs, indels, and internal and terminal deletions.
• Detection of TE variation and activity: Identifies clinal variation, interspecific TE diversity, recent TE invasions within populations, and hyperactive or inactive TE forms via sequence variation analysis.
• Sample types supported: Analyzes sequencing reads from tissue, individual, or population samples.
• Validation: Validated using publicly available datasets and simulated data to assess accuracy and reliability.
• Correction for internal deletions: Addresses underestimation of TE abundance caused by unaccounted internal deletions in naive approaches.

Scientific Applications:

• Evolutionary studies: Provides data to investigate the evolutionary dynamics and sequence diversity of transposons.
• Population genetics: Detects recent TE invasions and population-level variation relevant to genetic diversity and adaptation studies.
• Comparative genomics: Enables comparison of TE diversity across species to study genomic evolution.

Methodology:

DeviaTE accepts sequencing reads and consensus TE sequences as input, processes Illumina or Sanger reads to derive TE coverage and sequence characteristics, and contrasts TE coverage with single-copy genes while accounting for internal deletions.