Ltr_finder

Introduction

LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.

For more information, please check:
Home page: https://github.com/xzhub/LTR_Finder

Versions

  • 1.07

Commands

  • ltr_finder

  • check_result.pl

  • down_tRNA.pl

  • filter_rt.pl

  • genome_plot.pl

  • genome_plot2.pl

  • genome_plot_svg.pl

Module

You can load the modules by:

module load biocontainers
module load ltr_finder

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run ltr_finder on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ltr_finder
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers ltr_finder

ltr_finder 3ds_72.fa -P 3ds_72 -w2  > test/3ds_72_result.txt \
    |   genome_plot.pl test/