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index.md

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 A lot of genomics analysis is done using command-line tools for three reasons: 
-1) you will often be working with a large number of files,
-and working through the command-line rather than through a graphical user interface (GUI) allows you to automate repetitive tasks, 
-2) you
-will often need more compute power than is available on your personal computer, and connecting to and interacting with remote computers
-requires a command-line interface, and 
+1) you will often be working with a large number of files, and working through the command-line rather than 
+through a graphical user interface (GUI) allows you to automate repetitive tasks,  
+2) you will often need more compute power than is available on your personal computer, and 
+connecting to and interacting with remote computers requires a command-line interface, and  
 3) you will often need to customize your analyses and command-line tools often enable more 
 customization than the corresponding GUI tools (if in fact a GUI tool even exists).