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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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About using TGS data #27

Open xxYaaoo opened 5 months ago

xxYaaoo commented 5 months ago

Hello Dr.Chen,

I'm wondering if the ERVcaller could be used to input long-read sequencing? ( ..and any suggestion about how to adjust command parameters and any validation result of identification accuracy while applying TGS data?

Thank you~

xunchen85 commented 5 months ago

Hi,

Unfortunately it was designed to analyze short reads. There are tools for analyzing long reads, like GraffiTE (https://www.biorxiv.org/content/10.1101/2023.09.11.557209v1) or others.

One potential command parameter to adjust would be the "-S"; again it was not recommended.

Thanks, Xun

xxYaaoo commented 5 months ago

ok I got it ! Thank you for your reply！～