RepeatMasker 4.1.5-foss-2022a

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. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library derived from Repbase sequences ) and Repbase, a service of the Genetic Information Research Institute.

Accessing RepeatMasker 4.1.5-foss-2022a

To load the module for RepeatMasker 4.1.5-foss-2022a please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2022a
module load RepeatMasker/4.1.5-foss-2022a

BEAR Apps Version

2022a

Architectures

EL8-cascadelake — EL8-sapphirerapids

The listed architectures consist of two part: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

More Information

For more information visit the RepeatMasker website.

Dependencies

This version of RepeatMasker has a direct dependency on: foss/2022a h5py/3.7.0-foss-2022a HMMER/3.3.2-gompi-2022a Perl/5.34.1-GCCcore-11.3.0 Python/3.10.4-GCCcore-11.3.0 RMBlast/2.13.0-gompi-2022a TRF/4.09.1-GCCcore-11.3.0

Required By

This version of RepeatMasker is a direct dependent of: funannotate/1.8.17-foss-2022a

Other Versions

These versions of RepeatMasker are available on the BEAR systems (BlueBEAR and BEAR Cloud VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 12th August 2024