Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data

Version 1 : Received: 17 December 2020 / Approved: 18 December 2020 / Online: 18 December 2020 (14:53:44 CET)

A peer-reviewed article of this Preprint also exists.

Sohrab, V.; López-Díaz, C.; Di Pietro, A.; Ma, L.-J.; Ayhan, D.H. TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data. Genes 2021, 12, 224. Sohrab, V.; López-Díaz, C.; Di Pietro, A.; Ma, L.-J.; Ayhan, D.H. TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data. Genes 2021, 12, 224.

Journal reference: Genes 2021, 12, 224
DOI: 10.3390/genes12020224

Abstract

Transposable elements (TEs) are mobile genetic elements capable of rapidly altering the genome through their movements. The importance of TE activity has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs results in the growing number of bioinformatics software to identify insertion events. However, the application of existing TE finding tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we report a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software dependencies using four inputs that can be easily generated with popular variant calling pipelines. The external software requirements are BEDTools, SAMtools, and Picard. Necessary inputs include TEs present in the reference genome, binary paired-end alignment, reference genome index, and a list of TE names. We tested TEfinder pipeline among several evolving populations of Fusarium oxysporum generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis.

Subject Areas

transposable elements; mobile element insertion events; next generation sequencing (NGS); genome evolution

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