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Published May 19, 2023 | Version v1.1.0
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NBISweden/AGAT: AGAT-v1.1.0

  • 1. IRD
  • 2. Oregon State University
  • 3. @VEuPathDB
  • 4. European Bioinformatics Institute | EMBL-EBI


  • Update readme
  • add the AGAT version in the log using the AGAT header method
  • doc:
    • fix #306: update doc to remove --ct parameter related to gxf script, which is now handled by the config.yaml file
    • fix #312 remove JSON because now AGAT use YAML instead
    • fix #314 add information about how AGAT deal with stop codon feature when converting GFF to GTF
  • fix #297 modify output name/type
  • #303 revise gfx doc for clarity
  • #300 add new script in order to rename sequence identifiers.
  • add feature types in feature_levels.yaml: 3'-utr, 5'-utr, crispr, splice3, splice5
  • fix #329 - when creating L1 from L2 be sure the L1 ID used is not already used by a feature of another type.
  • fix #327 - avoid crash if CDS less than 3 nt in
  • fix #325 and improve related merge functions (see improved result of test gff_syntax 15). Fix error in keep_only_uniq_fromlist2 function to merge identical isoform and add merge suffix for merged attributes
  • fix #315 add skip_merge_l3 in feature_levels yaml file to handle which feature to skip at the check_all_level3_locations step (decide which type of feature to merge when overlapping)
  • fix #290 - deal with GeMoMA peculiar case where L3 is attached to L1 while L2 exists while L2 is also attached to L1. Parent attribute used as a locus_tag
  • fix #347 update end location only if longest
  • fix #350 improve AGAT to deal properly with peculiar Exonerate gff
  • fix #352 do not check feature when already removed from hash in merge_overlap_loci to avoid error


  • factorize functions _merge_overlap_features and merge_overlap_features to keep only the later
  • change miscCount uniqID and uniqIDtoType hashes into a single hash for code simplification
  • remove L1 and L2 for newly created IDs. Fix problem ID use several times in e.g. agat_sp_prokka_fix_fragmented_gene_annotations_1.gff output file (used by tRNA level1 gene created)
  • Improve check_gene_overlap_at_CDSthenEXON to work at l2 and l1 if no children, and rename it into check_feature_overlap_from_l3_to_l1.
  • add get_uniq_id function to make unique ID on the fly for spread features that can share identical IDs
  • use push in infosequential instead of omniscient for Push-L3-omiscient-3: level3 - Use Unique ID even for CDS to avoid confusion in location and level3 checks - remove strand when cloning L3 to create a l2 (see issue #350)



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