T-lex3

T-lex3 genotypes transposable element (TE) insertions and estimates their population frequencies from short-read whole-genome sequencing data.

Key Features:

• Algorithmic enhancement: Incorporates the BWA-MEM aligner for short-read mapping, enabling support for longer reads (>150 bp) and processing of high-throughput sequencing data.
• Improved genotyping accuracy: Implements new filtering steps and customizable parameters, including thresholds for minimum and maximum read counts and minimum number of strains required per TE genotype.
• Broad applicability: Validated across diverse organisms, including Drosophila melanogaster, humans, and rice, supporting genomes with varying sizes and TE contents.
• Accurate TE calls in plant genomes: Provides accurate TE calls within a plant genome in this version, extending applicability to botanical and agricultural genomes.

Scientific Applications:

• Population Genetics: Estimating TE frequencies within populations to study genetic variation.
• Evolutionary Biology: Investigating the impact of TEs on genome evolution and adaptation.
• Comparative Genomics: Comparing TE insertions among species or strains to identify evolutionary patterns.

Methodology:

Maps short-read sequences using the BWA-MEM aligner and applies enhanced filtering mechanisms with customizable read-count and strain-count thresholds to produce TE genotype calls.