T-lex

T-lex detects the presence or absence of annotated transposable element (TE) copies in genomes from next-generation sequencing (NGS) data and estimates population frequencies of individual TE insertions.

Key Features:

• Presence/absence detection: Analyzes NGS data to determine whether specific annotated TE copies are present or absent in sample genomes.
• Population frequency estimation: Computes estimates of population frequencies for individual TE insertions across multiple strains.
• Multi-strain processing: Processes NGS data from numerous resequenced strains to enable population-level analyses.
• Validation performance: Experimentally validated on two resequenced Drosophila melanogaster strains, detecting ~95% of previously identified TE insertions with sensitivity 100% and specificity 97%.
• Low-coverage behavior: Maintains accuracy for reliably identifiable TE copies at low sequencing coverage but shows increased 'no data' calls below 15× coverage.
• Input requirements: Requires a reference genome, annotations of individual TE copies, and NGS data.
• Scalability: Handles large datasets and multiple strains for population genomics studies.

Scientific Applications:

• TE population genomics: Estimating insertion frequencies and studying distribution of TEs across populations and strains.
• Genomic dynamics and evolution: Investigating the evolutionary impact and dynamics of TEs across populations.
• Annotation validation: Verifying presence of annotated TE copies in resequenced genomes, exemplified by Drosophila melanogaster validation.

Methodology:

Analyzes NGS data to ascertain presence or absence of specific annotated TE copies and computes population frequency estimates; validated on two resequenced Drosophila melanogaster strains yielding ~95% detection, sensitivity 100%, and specificity 97%, with increased 'no data' calls below 15× coverage.