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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