LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

作者：Shujun Ou, Ning Jiang · 发表于：Mobile DNA · 年份：2019 · DOI：10.1186/s13100-019-0193-0 · 被引用次数：262 · 研究领域：Chromosomal and Genetic Variations、Genomics and Phylogenetic Studies、Plant Disease Resistance and Genetics

Abstract Annotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a widely used program for the identification of LTR retrotransposons but its application on large genomes is hindered by its single-threaded processes. Here we report an accessory program that allows parallel operation of LTR_FINDER, resulting in up to 8500X faster identification of LTR elements. It takes only 72 min to process the 14.5 Gb bread wheat ( Triticum aestivum ) genome in comparison to 1.16 years required by the original sequential version. LTR_FINDER_parallel is freely available at https://github.com/oushujun/LTR_FINDER_parallel .