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.

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

See which versions of ltr_retriver are available:

$ module avail ltr_retriever

Load one version into your environment and run it:

$ module load ltr_retriever/2.9.0
$ LTR_retriever -h

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.

Notes from the sysadmin during installation:

$ 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