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First off this is MySQL 5.6 and MyISAM tables, run on a desktop with a 4.2GHZ I7 16GB RAM and RAID 0 Drives.

I have a few large tables anywhere between 250 million and 2 billion rows, with sizes ranging between 20 and 150 GB. How long should it take to add indexes, mostly on VARCHAR or BIGINT columns, and what is the fastest way to do it?
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There isn't a good answer for this, what I would do is to make a subset of your table (let's say 100,000 rows) and add indexes to it, while timing it. Then extrapolate out for the size of your other tables and that should give you a rough answer.
 
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