====== LTR_retriever ======

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.


===== Information =====

  * Version: 2.9.0
  * Added: February, 2022
  * Link: https://github.com/oushujun/LTR_retriever

===== Usage =====

See which versions of ltr_retriver are available:
<code>$ module avail ltr_retriever</code>

Load one version into your environment and run it:
<code>$ module load ltr_retriever/2.9.0
$ LTR_retriever -h</code>

**Note:** Please use the ''-threads'' option to tell LTR_retriever how many CPUs it should use or else it will automatically use four (4). This number should match the number of CPUs you requested in your SLURM batch allocation.

**Note:** You can run the supplementary Perl scripts directly, ie ''Age_est.pl'', ''cleanup.pl'', ''LTR_sum.pl'', etc without calling ''perl'' as the documentation suggests.

===== Installation ======

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ git clone https://github.com/oushujun/LTR_retriever.git -b v2.9.0
$ chmod +x LTR_retriever/bin/*.pl
$ sudo mkdir -p /export/apps/ltr_retriever/2.9.0
$ sudo cp -r LTR_retriever/* /export/apps/ltr_retriever/2.9.0</code>