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A good graphic design agency will not send you out on a job that you're ill-prepared to do. That's why many of them require proficiency tests on key software. You'll be given a set time limit to do a certain number of tasks in the programs you use.
There are some software certifications, such as the Adobe Certification Exam, that you can do on your own. You may find that a design staffing agency will still require that you pass their tests before they send you to a client.
It is possible in some cases to quickly bone up on software you don't know and still pass the test. However, it's better all around if you don't fudge your technical skills on your resume. If there's a popular skill that you're lacking, your agency may be able to connect you with a training course.