deletions | additions       diff --git a/Genome Assembly and Annotation.md b/Genome Assembly and Annotation.md  index 2003551..87e8ace 100644  --- a/Genome Assembly and Annotation.md  +++ b/Genome Assembly and Annotation.md 
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Now that you are in the folder where you want your genome assembly to appear, you are ready to run the program. First, type (don't hit return yet!):  /Applications/a5\_pipeline/bin/a5\_pipeline.pl /Applications/a5_pipeline/bin/a5_pipeline.pl    Then, drag and drop in the input file(s) into the same Terminal window (or type the path to them if you know it). Finally, type a name that will be used as part of all of your output files. So, your command line should look like this:  /Applications/a5\_pipeline/bin/a5\_pipeline.pl /Applications/a5_pipeline/bin/a5_pipeline.pl  SequenceFile1.fastq SequenceFile2.fastq MyGenome Once the program finishes running you will have a complete assembly located in the a5\_output folder.