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xunchen85 / ERVcaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexity, such as the entire RepBase database. It is easy to install and use with command lines.
http://www.uvm.edu/genomics/software/ERVcaller.html
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关于SE_MEI的问题 #14

Open ChristopherLeeZG opened 2 years ago

ChristopherLeeZG commented 2 years ago

你好，陈博，readme里面写到本软件会包含SE_MEI的脚本，但是我并没有看到。 于是我到SE_MEI原作者的GitHub里面下载安装了SE_MEI（改了htslib的版本为1.1），可以跑通ERVcaller，请问这也可以吗。 谢谢大神！

xunchen85 commented 2 years ago

您好，你可以在ERVcaller软件的Scripts/ 文件夹下面找到对应的压缩文件。原始版本的SE_MEI script并不能产生所需要的信息，因此尽管可以跑通ERVcaller，也无法有效使用split reads

chen

ChristopherLeeZG commented 2 years ago

好的，谢谢陈博！