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LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences.
Eric Disdero1, Jonathan Filée1
1Laboratoire Evolution, Génomes, Comportement, Ecologie; CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France.
Mobile DNA
|April 14, 2017
Summary
A new tool, LoRTE, analyzes transposable element (TE) insertions and deletions using long read sequencing. This advances population genomics by overcoming limitations of short-read technologies for studying TE dynamics.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Transposable elements (TEs) are crucial in population genomics.
- Short-read sequencing technologies face limitations in analyzing TEs due to their repetitive nature.
- Long-read sequencing offers potential for comprehensive TE analysis.
Purpose of the Study:
- To develop a novel bioinformatic tool for analyzing transposable element insertions and deletions using long-read sequencing data.
- To address the limitations of existing software in handling long reads for population genomic studies of TEs.
Main Methods:
- Development of LoRTE, a software tool specifically designed for long-read sequencing data (e.g., PacBio).
- Utilized simulated and real PacBio datasets of *Drosophila melanogaster* for testing.
- Focused on identifying TE deletions and insertions by comparing sample genomes to a reference genome.
Main Results:
- LoRTE is the first tool capable of identifying TE deletions and insertions using PacBio long reads.
- The tool demonstrated reliability and broad applicability in analyzing *Drosophila melanogaster* datasets.
- LoRTE effectively utilizes low-coverage, long-read sequences for studying TE dynamics.
Conclusions:
- LoRTE is an efficient and accurate tool for identifying structural genomic variants resulting from TE activity.
- The software facilitates the study of the evolutionary impact of transposable elements.
- LoRTE is publicly available for download, promoting further research in the field.