Edta

Introduction

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

For more information, please check its website: https://biocontainers.pro/tools/edta and its home page on Github.
Note: Running EDTA, please use the command like this:

EDTA.pl [OPTIONS]

DO NOT call it ‘perl EDTA.pl’

Versions

  • 1.9.6

  • 2.0.0

Commands

  • EDTA.pl

  • EDTA_processI.pl

  • EDTA_raw.pl

  • FET.pl

  • bdf2gdfont.pl

  • buildRMLibFromEMBL.pl

  • buildSummary.pl

  • calcDivergenceFromAlign.pl

  • cd-hit-2d-para.pl

  • cd-hit-clstr_2_blm8.pl

  • cd-hit-div.pl

  • cd-hit-para.pl

  • check_result.pl

  • clstr2tree.pl

  • clstr2txt.pl

  • clstr2xml.pl

  • clstr_cut.pl

  • clstr_list.pl

  • clstr_list_sort.pl

  • clstr_merge.pl

  • clstr_merge_noorder.pl

  • clstr_quality_eval.pl

  • clstr_quality_eval_by_link.pl

  • clstr_reduce.pl

  • clstr_renumber.pl

  • clstr_rep.pl

  • clstr_reps_faa_rev.pl

  • clstr_rev.pl

  • clstr_select.pl

  • clstr_select_rep.pl

  • clstr_size_histogram.pl

  • clstr_size_stat.pl

  • clstr_sort_by.pl

  • clstr_sort_prot_by.pl

  • clstr_sql_tbl.pl

  • clstr_sql_tbl_sort.pl

  • convert_MGEScan3.0.pl

  • convert_ltr_struc.pl

  • convert_ltrdetector.pl

  • createRepeatLandscape.pl

  • down_tRNA.pl

  • dupliconToSVG.pl

  • filter_rt.pl

  • genome_plot.pl

  • genome_plot2.pl

  • genome_plot_svg.pl

  • getRepeatMaskerBatch.pl

  • legacy_blast.pl

  • lib-test.pl

  • make_multi_seq.pl

  • maskFile.pl

  • plot_2d.pl

  • plot_len1.pl

  • rmOut2Fasta.pl

  • rmOutToGFF3.pl

  • rmToUCSCTables.pl

  • update_blastdb.pl

  • viewMSA.pl

  • wublastToCrossmatch.pl

Module

You can load the modules by:

module load biocontainers
module load edta

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 Edta on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 10
#SBATCH --job-name=edta
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers edta

EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib EDTA/database/rice6.9.5.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10