RepeatMasker软件是library-based，通过相似性比对来识别重复序列，可以屏蔽序列中转座子重复序列和低复杂度序列（默认将其替换成N）。使用数据库Dfam和Repbase
The Dfam database is a collection of Repetitive DNA element sequence alignments, hidden Markov models (HMMs) and matches lists for complete Eukaryote genomes.
Repbase是由美国遗传信息研究所（GIRI）创建并维护，收录了转座子和其他重复序列及其注释信息。
本地安装RepeatMasker，除了需要RepeatMasker主程序外，还需要TRF（Tandem Repeats Finder）、序列搜索引擎（以RMBlast为例）以及Repbase数据库。
搜索引擎可以安装多个，但是每次只能用一个。
Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
要屏蔽的区域：low-complexity DNA sequences and interspersed repeats
比对引擎：cross_match WU-BLAST(更快)
阈值设定：
-lib 指定数据库
-nolow 不去mask low-complexity DNA or simple repeats
-no_is Skips bacterial insertion element check
-norna Does not mask small RNA (pseudo) genes
速度设定
-s Slow search; 0-5% more sensitive, 2-3 times slower than default
-q Quick search; 5-10% less sensitive, 2-5 times faster than default
-qq Rush job; about 10% less sensitive, 4->10 times faster than default
(quick searches are fine under most circumstances) repeat options
参考来源
https://www.cnblogs.com/pxy7896/p/10008578.html