It's 2020 and many of these answers no longer apply to the Sequelize v4/v5/v6 ecosystem.
The one good answer says to use sequelize-auto-migrations, but probably is not prescriptive enough to use in your project. So here's a bit more color...
Setup
My team uses a fork of sequelize-auto-migrations because the original repo is has not been merged a few critical PRs. #56 #57 #58 #59
$ yarn add github:scimonster/sequelize-auto-migrations#a063aa6535a3f580623581bf866cef2d609531ba
Edit package.json:
"scripts": {
  ...
  "db:makemigrations": "./node_modules/sequelize-auto-migrations/bin/makemigration.js",
  ...
}
Process
Note: Make sure you’re using git (or some source control) and database backups so that you can undo these changes if something goes really bad.
- Delete all old migrations if any exist.
- Turn off .sync()
- Create a mega-migration that migrates everything in your current models (yarn db:makemigrations --name "mega-migration").
- Commit your 01-mega-migration.jsand the_current.jsonthat is generated.
- if you've previously run .sync()or hand-written migrations, you need to “Fake” that mega-migration by inserting the name of it into your SequelizeMeta  table.INSERT INTO SequelizeMeta Values ('01-mega-migration.js').
- Now you should be able to use this as normal…
- Make changes to your models (add/remove columns, change constraints)
- Run $ yarn db:makemigrations --name whatever
- Commit your 02-whatever.jsmigration and the changes to_current.json, and_current.bak.json.
- Run your migration through the normal sequelize-cli: $ yarn sequelize db:migrate.
- Repeat 7-10 as necessary
Known Gotchas
- Renaming a column will turn into a pair of removeColumnandaddColumn. This will lose data in production. You will need to modify the up and down actions to userenameColumninstead.
For those who confused how to use renameColumn, the snippet would look like this. (switch "column_name_before" and "column_name_after" for the rollbackCommands)
{
    fn: "renameColumn",
    params: [
        "table_name",
        "column_name_before",
        "column_name_after",
        {
            transaction: transaction
        }
    ]
}
- If you have a lot of migrations, the down action may not perfectly remove items in an order consistent way. 
- The maintainer of this library does not actively check it. So if it doesn't work for you out of the box, you will need to find a different community fork or another solution.