The script allows to generate a tabulated format report of repeats annotated from a gff file containing repeats (feature type must be match or protein_match).

SYNOPSIS -i <input file> [-g <integer or fasta> -o <output file>] --help


  • -i, --gff, --file or --input

    STRING: Input GTF/GFF file(s). Several files can be processed at once: -i file1 -i file2

  • -g, --genome

    That input is design to know the genome size in order to calculate the percentage of the genome represented by each kind of repeats. You can provide an INTEGER or the genome in fasta format. If you provide the fasta, the genome size will be calculated on the fly.

  • -o or --output

    STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format.

  • -c or --config

    String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

  • --help or -h

    Display this helpful text.