When comparing GitHub Issues vs JIRA, the Slant community recommends GitHub Issues for most people. In the question“What are the best bug/issue tracking tools for small development teams?” GitHub Issues is ranked 5th while JIRA is ranked 14th. The most important reason people chose GitHub Issues is:
GitHub has added another layer of security to their user accounts. This layer comes in the form of Two-Factor authentication. After it's enabled, GitHub delivers an authentication code by SMS, or by a [free application for smartphones](https://help.github.com/articles/configuring-two-factor-authentication-via-a-totp-mobile-app/). After two-factor authentication is enabled, the authentication code is sent to the account owner's phone any time someone attempts to sign into their GitHub account. This means that only someone who has both the password and authentication code can sign into the account.
Ranked in these QuestionsQuestion Ranking
Pro Supports Two-Factor authentication
GitHub has added another layer of security to their user accounts. This layer comes in the form of Two-Factor authentication. After it's enabled, GitHub delivers an authentication code by SMS, or by a free application for smartphones. After two-factor authentication is enabled, the authentication code is sent to the account owner's phone any time someone attempts to sign into their GitHub account. This means that only someone who has both the password and authentication code can sign into the account.
Pro Convenient continuous integration with Travis CI
GitHub can be integrated with Travis CI for code testing and it is free for free open-source projects.
Pro Simplified team management tools
GitHub has easy and useful features to control teams, large and small alike. Team members can be given different powers on different projects, ranging from the ability to create them, to only being able to have read-only access.
Pro Large community
GitHub is the largest code host on the planet with over 21.4 million hosted repositories and many users. It's unarguably the largest VCS used by developers worldwide and as such, it has a vibrant community that follows it resulting in many guides and tutorials for new users. Even experienced developers can always find an answer to any question they may have.
Pro Nice and usable UI
GitHub's UI is clean and intuitive. Each view is designed to not fill the screen with useless information.
For example, the repository view displays only the most crucial data about that repo - on the top it displays the number of commits, branches, releases and contributors. When clicked, each of them will take the user to a page that displays more detailed information.
Pro Anyone can fork
Any user can fork a project and submit a pull request. If accepted by the owner, the fork will be merged with the master branch.
Pro Excellent native apps
GitHub has native apps for mobile (iOS and Android), Windows and Mac, which make code deployment easier and faster.
Pro Lots of integrations and plugins
It integrates well with a lot of other tools, including other products from the Atlassian suite. Plus there are a ton of plugins, including charting tools, screen capture, etc.
Pro Backed by a trustable company
Jira is developed and maintained by Atlassian, which is not an unknown venture, especially for developers. Atlassian has a great number of other products used by million of users worldwide, including BitBucket, HipChat, Confluence and Stash.
Each of these products have hundreds of thousands of users who use them daily and this has allowed Atlassian to garner a lot of goodwill from the dev community.
Pro Very cheap for small teams
Pro Supports version-focused work-flows
JIRA is not a plain long list of tickets, but can be configured to be version-focused, so planning and understanding the progress in a software project becomes clear.
Pro Great reporting tools
Jira offers amazingly powerful reporting tools like activity stream, different graphs of opened and closed issues over time etc...
Con Issues are not systematically linked to a specific release
Con Only git repositories are fully supported
Github has full support only for Git, while it has some support for SVN. But it doesn't have any support for Mercurial though.
Con Proprietary tool
Con Only public repositories are free
Unfortunately, compared to some other competitors, GitHub offers closed repositories only for premium users, and the price is not cheap at all.
Con New releases often change the GUI largely
Sometimes the usage becomes worse, e.g. when creating a new ticket, you need to click the notification to keep it on the display.
Con Locks you inside its own ecosystem
If you use Jira you are pretty much locked inside their ecosystem. For example, if you want to add a tool to your project management stack (like a wiki) more often than not you will have to buy one of Atlassian's tools.
Con Client application support
No free client applications; IDE connector development was discontinued. Users are effectively locked into using web interface which requires context-switching.