Software: edta
Description
Edta is is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.
Available Versions
| Unspecified: | 1.9.6 2.0.0 |
|---|
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'
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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