Repeatmasker Tables HardmaskedPart 2

We annotated repeats in assemblies through two rounds of annotation with RepeatMasker4.1.0 (Smit et al. 2020), the first round used custom repeat libraries generated by RepeatModeler2 for each respective assembly and with search engine “ncbi” and option -xsmall. We then converted the softmasked assembly resulting from the first RepeatMasker round to a hardmasked assembly using the lc2n.py script (https://github.com/PdomGenomeProject/repeat-masking), and re-ran RepeatMasker on the hard-masked assembly with RepeatMasker’s internal arthropod repeat library and species “Arthropoda”. We then merged RepeatMasker output tables from both runs to summarize the abundance of RE categories. Authors: John S. Sproul, Scott Hotaling, Jacqueline Heckenhauer, Ashlyn Powell, Amanda M. Larracuente, Joanna L. Kelley, Steffen U. Pauls, and Paul B. Frandsen本研究借助RepeatMasker4.1.0软件（Smit等，2020）开展两轮重复序列注释，以完成基因组组装序列中的重复序列标注工作。第一轮注释采用针对每个对应组装序列由RepeatModeler2生成的自定义重复序列库，设置搜索引擎为“ncbi”，并启用参数-xsmall。随后，我们使用lc2n.py脚本（开源地址：https://github.com/PdomGenomeProject/repeat-masking）将第一轮RepeatMasker运行得到的软屏蔽基因组组装序列转换为硬屏蔽基因组组装序列；接着针对硬屏蔽后的组装序列，使用RepeatMasker内置的节肢动物重复序列库，以物种“Arthropoda”为分类目标再次运行RepeatMasker。最后，我们合并两轮RepeatMasker的输出表格，以统计重复元件（Repetitive Elements, RE）各类别的丰度信息。作者：John S. Sproul、Scott Hotaling、Jacqueline Heckenhauer、Ashlyn Powell、Amanda M. Larracuente、Joanna L. Kelley、Steffen U. Pauls 与 Paul B. Frandsen