Revision as of 21:24, 6 December 2019

Description

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.

Required Modules

modules documentation

Serial

repeatmasker

System Variables

HPC_REPEATMASKER_DIR - installation directory

Validation

Validated 4/5/2018

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 __NOEDITSECTION__
 [[Category:Software]][[Category:Bioinformatics]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|repeatmasker}}
 |{{#vardefine:url|http://www.repeatmasker.org/}}
-<!--Compiler and MPI settings - OPTIONAL -->
-|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
-<!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
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 performed by one of several popular search engines including,
 cross_match, ABBlast/WUBlast, RMBlast and Decypher.
+<!--Modules-->
-==Available Versions==
+==Required Modules==
-* 3.3.0
+[[Modules|modules documentation]]
-<!-- -->
+===Serial===
-{{#if: {{#var: mod}}|==Running the application using modules==
+*{{#var:app}}
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 {{#if: {{#var: exe}}|==How To Run==
 WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 {{#if: {{#var: testing}}|==Performance==
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 WRITE CITATION HERE
 |}}
+=Validation=
+* Validated 4/5/2018

Difference between revisions of "RepeatMasker"