agat_sq_repeats_analyzer.pl

DESCRIPTION

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

agat_sq_repeats_analyzer.pl -i <input file> [-g <integer or fasta> -o <output file>]
agat_sq_repeats_analyzer.pl --help

OPTIONS

• -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.

• --help or -h

  Display this helpful text.