The script adds start and stop codons when a CDS feature exists. The script looks at the nucleotide sequence and checks the presence of start and stop codons. The script works even if the start or stop codon are split over several CDS features.

SYNOPSIS --gff infile.gff --fasta genome.fa --out outfile.gff --help


  • --gff, -i or -g

    Input GTF/GFF file.

  • --fasta, --fa or -f

    Input fasta file. Needed to check that CDS sequences start by start codon and stop by stop codon.

  • --ct, --codon or --table

    Codon table to use. [default 1]

  • --out, --output or -o

    Output gff file updated

  • -v

    Verbose for debugging purpose.

  • --help or -h

    Display this helpful text.