Tools

The DENOFO toolkit comprises three main tools, each available in both a command-line interface (CLI) and a graphical user interface (GUI):

1. denofo-questionnaire: Interactively guides the user through a series of questions, saving the resulting annotation in a *.dngf file.

2. denofo-converter: Converts annotations between different file types. For example, it can annotate sequences in a *.fasta or *.gff file with an existing *.dngf annotation file using a short string encoding.

3. denofo-comparator: Compares two annotation files, highlighting similarities and differences in methodology.

Both CLI and GUI versions are provided to cater to different user needs and environments. The CLI tools are suitable for remote servers, HPC environments without display, and automated pipelines. The GUI tools offer an intuitive interface for users without extensive command-line experience.