Issue tracking: Jira all the way.... Very powerful for issue tracking. Building a backlog is easy, prioritizing it is a breeze, and organizing sprints is not a pain. Even things like assigning work hours (which I know some companies take seriously.... why, I have no idea) can be done with Jira. Custom issue types, and ease of everything is another huge plus for us. For Agile, this is probably the best tool you have.
Documentation: Confluence! This is one of my favorite parts of the development side-stack. Confluence offers us a single place to keep all our documentation, add comments, edit and update pages etc. It also allows for personal spaces, which is a pretty nifty feature. The only option I'd look at other than Confluence for team document sharing is setting up of a Wiki. Small things like support for wiki markup, anchoring pages, setting up of spaces etc. makes Confluence a winner in my eyes!
Sprinting: During the sprint, our dashboard runs GreenHopper. In a single view, we can see how the sprint is going. Which tasks are complete, which are being worked upon, which are yet to be started. Besides the burndown chart, which just tells you a top view of how a sprint is doing, GreenHopper allows you to see the details of the sprint stories.
Though I've never used Rally, I know of a couple of teams that have, over the last two months or so, switched to the Atlassian stack, and so far, I haven't heard any of them complain about anything specific. You may probably also want to check out Planbox, though mostly Jira and Rally seem to be the key players in the race.
Github, I think works great for side projects (i personally use it), but I really doubt how well it works for large enterprise projects. Ofcourse, if you're talking about a CVS, then you need to consider git, svn, mercurial, perforce etc. before taking a decision, but I doubt Github will be of much use. Also, considering you have options like Gitlab, I don't see why any lareg enterprise would need Github (though being a Github fanboi, I hope the use case emerges).
End of the day, all all tools are just meant to help you... so go with whatever the team is comfortable with! If it doesn't work for you, change it after a few iterations... isn't that what Agile is about anyway? :) :P
Read full article from (4) Agile Software Development: Which is better for a large enterprise, Greenhopper / Jira / Atlassian or Rally or github? Or someone else? - Quora
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