Heat oven to 375 degrees. Split butternut squash length-wise and scoop out the seeds. Sprinkle squash with a dash of salt and olive oil. Roast in the oven for 1 hour or until fork-tender.
While the squash is roasting, roughly chop shallot and garlic. Sautee both in a glug of oil in a small skillet until soft. Remove from heat.
When the squash has finished roasting, peel away the skin and reserve the flesh. Add it to a high-powered blender or food processor, along with shallot/garlic mixture, nutritional yeast, soaked (and drained) cashews, water and salt. Whiz on high until sauce is extra smooth and creamy.
Cook pasta according to package instructions and toss in a large bowl with the sauce. Sprinkle with chili flakes and black pepper. Serve warm.