deletions | additions       diff --git a/Genome Assembly and Annotation.md b/Genome Assembly and Annotation.md  index 11d6f56..31e3469 100644  --- a/Genome Assembly and Annotation.md  +++ b/Genome Assembly and Annotation.md 
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After downloading and unzipping the program, change the name of the folder to a5\_pipeline and move it from your downloads folder to your Applications folder. Then, create a new folder which will contain the files generated by the pipeline on your Desktop. By the way, there's nothing special about having your file on the Desktop, it's just there to simplify our instructions. We will refer to this folder as "a5_output", but you should use a more informative name.  ###Running A5 A5-miseq  Open a Terminal window and navigate to a5\_output. A5 A5-miseq  will write all of the assembly output files to the same folder from which you run the program. In this example the newly created folder is on the Desktop and named a5_ouput a5_output  so the syntax for navigating to the folder in a Terminal window is cd Desktop/a5_output/ 
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Among the numerous files generated by A5, two of particular importance are the "MyGenome.contigs.fasta" and "MyGenome.final.scaffolds.fasta" which contain the contigs and scaffolds, respectively.  In addition, A5 A5-miseq  generates a file containing information about the quality of the assembly called "MyGenome.assembly_stats.csv" To view this file use the "less" command: