Welcome to AGAT's documentation!
AGAT: Another GTF/GFF Analysis Toolkit
A GFF/GTF toolkit allowing you to perform almost everything you might want to achieve ^^
The GTF/GFF formats are 9-column text formats used to describe and represent genomic features. The formats have quite evolved since 1997, and despite well-defined specifications existing nowadays they have a great flexibility allowing holding wide variety of information. This flexibility has a drawback aspect, there is an incredible amount of flavor of the formats: GFF / GFF1 / GFF2 / GFF2.5 / GFF3 / GTF / GTF2 / GTF2.1 / GTF2.2 / GTF2.5 / GTF3
It's often hard to understand and differentiate all GFF/GTF formats/flavors. Many tools using GTF/GFF formats fails due to specific expectations. AGAT is a suite of tools able to deal with any GTF/GFF formats and perform most of the possible tasks you would need.
Contents
General
- What can AGAT do for you?
- How does AGAT work?
- Troubleshooting
- AGAT throws features out, because the feature type is not yet taken into account
- AGAT throws features out, because child features are not provided
- How to use a version of AGAT from a specific branch
- How to fix Bio::Root::Exception met in AGAT
- How to use codon table 0 (codon table 1 is used instead)?
- Why when asking for table 0 AGAT keep using the table 1 ?
- How to cite?
- Why AGAT?
Knowledge
AGAT vs other tools
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