Agat

Introduction

Agat is a suite of tools to handle gene annotations in any GTF/GFF format.

For more information, please check its website: https://biocontainers.pro/tools/agat and its home page on Github.

Versions

  • 0.8.1

Commands

  • agat_convert_bed2gff.pl

  • agat_convert_embl2gff.pl

  • agat_convert_genscan2gff.pl

  • agat_convert_mfannot2gff.pl

  • agat_convert_minimap2_bam2gff.pl

  • agat_convert_sp_gff2bed.pl

  • agat_convert_sp_gff2gtf.pl

  • agat_convert_sp_gff2tsv.pl

  • agat_convert_sp_gff2zff.pl

  • agat_convert_sp_gxf2gxf.pl

  • agat_sp_Prokka_inferNameFromAttributes.pl

  • agat_sp_add_introns.pl

  • agat_sp_add_start_and_stop.pl

  • agat_sp_alignment_output_style.pl

  • agat_sp_clipN_seqExtremities_and_fixCoordinates.pl

  • agat_sp_compare_two_BUSCOs.pl

  • agat_sp_compare_two_annotations.pl

  • agat_sp_complement_annotations.pl

  • agat_sp_ensembl_output_style.pl

  • agat_sp_extract_attributes.pl

  • agat_sp_extract_sequences.pl

  • agat_sp_filter_by_ORF_size.pl

  • agat_sp_filter_by_locus_distance.pl

  • agat_sp_filter_by_mrnaBlastValue.pl

  • agat_sp_filter_feature_by_attribute_presence.pl

  • agat_sp_filter_feature_by_attribute_value.pl

  • agat_sp_filter_feature_from_keep_list.pl

  • agat_sp_filter_feature_from_kill_list.pl

  • agat_sp_filter_gene_by_intron_numbers.pl

  • agat_sp_filter_gene_by_length.pl

  • agat_sp_filter_incomplete_gene_coding_models.pl

  • agat_sp_filter_record_by_coordinates.pl

  • agat_sp_fix_cds_phases.pl

  • agat_sp_fix_features_locations_duplicated.pl

  • agat_sp_fix_fusion.pl

  • agat_sp_fix_longest_ORF.pl

  • agat_sp_fix_overlaping_genes.pl

  • agat_sp_fix_small_exon_from_extremities.pl

  • agat_sp_flag_premature_stop_codons.pl

  • agat_sp_flag_short_introns.pl

  • agat_sp_functional_statistics.pl

  • agat_sp_keep_longest_isoform.pl

  • agat_sp_kraken_assess_liftover.pl

  • agat_sp_list_short_introns.pl

  • agat_sp_load_function_from_protein_align.pl

  • agat_sp_manage_IDs.pl

  • agat_sp_manage_UTRs.pl

  • agat_sp_manage_attributes.pl

  • agat_sp_manage_functional_annotation.pl

  • agat_sp_manage_introns.pl

  • agat_sp_merge_annotations.pl

  • agat_sp_prokka_fix_fragmented_gene_annotations.pl

  • agat_sp_sensitivity_specificity.pl

  • agat_sp_separate_by_record_type.pl

  • agat_sp_statistics.pl

  • agat_sp_webApollo_compliant.pl

  • agat_sq_add_attributes_from_tsv.pl

  • agat_sq_add_hash_tag.pl

  • agat_sq_add_locus_tag.pl

  • agat_sq_count_attributes.pl

  • agat_sq_filter_feature_from_fasta.pl

  • agat_sq_list_attributes.pl

  • agat_sq_manage_IDs.pl

  • agat_sq_manage_attributes.pl

  • agat_sq_mask.pl

  • agat_sq_remove_redundant_entries.pl

  • agat_sq_repeats_analyzer.pl

  • agat_sq_rfam_analyzer.pl

  • agat_sq_split.pl

  • agat_sq_stat_basic.pl

Module

You can load the modules by:

module load biocontainers
module load agat

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 Agat on our our clusters:

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

module --force purge
ml biocontainers agat

agat_convert_sp_gff2bed.pl  --gff genes.gff -o genes.bed