Optional parameters

BLAST integration (optional)

If BLAST+ and a local database are available, the pipeline can include BLAST hit tables in the report and write a *_blast.tsv file.

See Using local BLAST.

Primer trimming/orientation

The current workflow relies on MAFFT’s orientation adjustment. Primer trimming and explicit orientation checks may exist as CLI/GUI arguments for future work, but are not required for the current default path.

Advanced GUI-only toggles

Depending on the desktop wrapper you use, you may also see options like:

  • “Create timestamped run folder”

  • “Save intermediate files”

  • “Force rerun”

These do not change the underlying scientific pipeline logic; they control file management and reproducibility behavior.