uhhhhh, I got to the point where I learn that the universe is dying and that I can go to the center of the galaxy to purge it, I don’t know what the ATLAS sequence counter is
That means you haven't completed the questline yet. Every time you travel to any new star system, the counter will increase and you will gain a portal glyph. Once the counter reaches 16, a portal to the final Atlas interface will be revealed.