How do I set the default stringency for hiding the low-quality ends of sequence traces (chromatograms) when aligning to a reference DNA sequence?
Open Preferences
Click SnapGene → Preferences (macOS) or Edit → Preferences (Windows or Linux), and select "Traces & Alignment" in the sidebar.
Use the drop-down menu to set the desired default stringency for hiding the low-quality ends.
Note that you can adjust this parameter at any time when working with an alignment to a reference DNA sequence — see Adjust Hiding of Chromatogram Ends.