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

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

Ou, Shujun; Jiang, Ning

Mobile DNA, 12/2019, Volume: 10, Issue: 1

Journal Article

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 ( ) 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.

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Ou, Shujun | Jiang, Ning

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