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repeatmasker-software

RepeatMasker

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). Currently over 56% of human genomic sequence is identified and masked by the program.

Information

Usage

See versions of repeatmasker which are available:

$ module avail repeatmasker

Load one version into your environment and run it:

$ module load repeatmasker/4.1.1
$ RepeatMasker

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.1.tar.gz
$ tar xf RepeatMasker-4.1.1.tar.gz
$ sudo mkdir -p /export/apps/repeatmasker/4.1.1
$ sudo chown aorth:aorth /export/apps/repeatmasker/4.1.1
$ python3 -m venv /export/apps/repeatmasker/4.1.1/venv
$ source /export/apps/repeatmasker/4.1.1/venv/bin/activate
$ pip install h5py
$ cp -r RepeatMasker/* /export/apps/repeatmasker/4.1.1
$ cd /export/apps/repeatmasker/4.1.1
# Here you have to manually enter the paths to trf, hmmer, and rmblast
$ perl ./configure
$ deactivate
$ sudo chown -R root:root /export/apps/repeatmasker/4.1.1
repeatmasker-software.txt · Last modified: 2020/11/01 15:04 by aorth