期刊
MOBILE DNA
卷 10, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s13100-019-0193-0
关键词
Genome annotation; Transposable element; LTR retrotransposon; LTR_FINDER
资金
- National Science Foundation [IOS-1740874]
- United States Department of Agriculture National Institute of Food and Agriculture
- AgBioResearch at Michigan State University [MICL02408]
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.
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