RelocaTE2

From UFRC
Revision as of 20:32, 14 January 2020 by Maxprok (talk | contribs) (Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|relocate2}} |{{#vardefine:url|https://github.com/JinfengChen/RelocaTE2}} <!-...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Description

relocate2 website  

RelocaTE2 is an improved version of RelocaTE (Robb et al., 2013). RelocaTE2 is highly sensitive and accurate in mapping transposable elements (TE) polymorphisms at single base pair resolution. RelocaTE2 uses the reads associated with TEs as seeds to cluster the read pairs on chromosomes. It automatically detects the target site duplication (TSD) of a TE insertion from alignments in each cluster, which enable high resolution mapping of TE polymorphisms. Unlike parallel searching of multi-TE elements in RelocaTE, RelocaTE2 searches all TEs in one cycle, which enables us find polymorphisms of thousands of TEs in an individual genome or large population in a reasonable timeframe without losing sensitivity and specificity.

Environment Modules

Run module spider relocate2 to find out what environment modules are available for this application.

System Variables

  • HPC_RELOCATE2_DIR - installation directory
  • HPC_RELOCATE2_EXE - executable directory






Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=RelocaTE2&oldid=20000"