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