RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including, cross_match, ABBlast/WUBlast, RMBlast and Decypher.
Running the application using modules
To use repeatmasker with the environment modules system at HPC the following commands are available:
Get module information for repeatmasker:
$module spider repeatmasker
Load the default application module:
$module load repeatmasker
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_REPEATMASKER_DIR - directory where repeatmasker is located.