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

Abstract

SummaryAnnotation 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 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 up to 8,500X faster identification of LTR elements. It takes only 72 minutes to process the 14.5 Gb bread wheat (Triticum aestivum) genome in comparison to 1.16 years required by the original sequential version.\n\nAvailabilityLTR_FINDER_parallel is freely available at https://github.com/oushujun/LTR_FINDER_parallel.\n\nContactjiangn@msu.edu