Difference between revisions of "EDTA"

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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
  
 
<!--Configuration-->
 
<!--Configuration-->

Latest revision as of 21:20, 6 December 2019

Description

edta website  

This package is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.

For the initial search of TE candidates, LTRharvest, LTR_FINDER_parallel, and LTR_retriever are incorporated in this package to identify LTR retrotransposons; GenericRepeatFinder, TIR-Learner, and MITE-Hunter are incorporated in this package to identify TIR transposons (a subclass of DNA transposons); HelitronScanner is incorporated in this package to identify Helitron transposons (a subclass of DNA transposons); and finally RepeatModeler is used to identify any TEs missed by these structure-based programs (such as SINEs and LINEs).

The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.

For benchmarking of a testing TE library, I have provided the curated TE annotation (v6.9.5) for the rice genome (TIGR7/MSU7 version). You may use the lib-test.pl script to compare the annotation performance of your method/library to the methods we have tested (usage shown below).

Environment Modules

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

System Variables

  • HPC_EDTA_DIR - installation directory
  • HPC_EDTA_BIN - executable directory