TEMP

TEMP detects transposable element insertions and excisions from pooled high-throughput sequencing data by combining pair-end reads and split reads.

Key Features:

• Insertion and excision detection: TEMP identifies both the presence and absence of TE insertions in genomic DNA sequences derived from heterogeneous samples.
• Frequency estimation: TEMP accurately estimates the frequencies of transposition events in the population.
• Junction pinpointing: TEMP pinpoints junctions of high frequency transposition events at nucleotide resolution.
• Performance benchmarking: TEMP outperforms PoPoolationTE, RetroSeq, VariationHunter and GASVPro on simulation data.

Scientific Applications:

• Population genomics: TEMP characterizes TE frequencies in wild Drosophila melanogaster populations.
• Hybrid dysgenesis studies: TEMP studies the inheritance patterns of TEs during hybrid dysgenesis.
• Molecular effect identification: TEMP identifies sequence signatures of TE insertion and possible molecular effects of TE movements, such as altered gene expression and piRNA production.
• Human genomics: TEMP performs on whole-genome human data derived from the 1000 Genomes Project.

Methodology:

TEMP combines information provided by pair-end reads and split reads to detect TE movements present with a wide range of frequencies in a population.