AGAT
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General

  • What can AGAT do for you?
  • How does AGAT work?
  • Troubleshooting
  • How to cite?
  • Why AGAT?

Knowledge

  • The GTF/GFF formats

AGAT vs other tools

  • Topological sorting of gff features
  • GFF to BED conversion
  • GFF to GTF conversion

List of tools

  • 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_intergenic_regions.pl
  • agat_sp_add_introns.pl
  • agat_sp_add_splice_sites.pl
  • agat_sp_add_start_and_stop.pl.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_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_lift_coverage.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_move_attributes_within_records.pl
  • agat_sp_prokka_fragmented_gene_annotations.pl
  • agat_sp_sensitivity_specificity.pl
  • agat_sp_separate_by_record_type.pl
  • agat_sp_split_by_level2_feature.pl
  • agat_sp_statistics.pl
  • agat_sp_to_tabulated.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_filter_feature_from_fasta.pl
  • agat_sq_list_attributes.pl
  • agat_sq_manage_ID.pl
  • agat_sp_manage_attributes.pl
  • agat_sq_mask.pl
  • agat_sq_remove_redundant_entries.pl
  • agat_sq_repeats_analyzer.pl
  • agat_sq_reverse_complement.pl
  • agat_sq_rfam_analyzer.pl
  • agat_sq_split.pl
  • agat_sq_stat_basic.pl
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