deletions | additions       diff --git a/Genome Assembly and Annotation.md b/Genome Assembly and Annotation.md  index e44f925..b6c65f2 100644  --- a/Genome Assembly and Annotation.md  +++ b/Genome Assembly and Annotation.md 
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a5_pipeline.pl read_1.fastq read_2.fastq mygenome  /Users/Madison/Desktop/a5_miseq_macOS_20140113/bin/a5_pipeline.pl /Users/Madison/Desktop/a5\_miseq\_macOS\_20140113/bin/a5\_pipeline.pl  is the pipeline and its location /Users/Madison/Desktop/a5_miseq_macOS_20140113/example/phiX_p1.fastq is the first paired end read  /Users/Madison/Desktop/a5_miseq_macOS_20140113/example/phiX_p2.fastq is the second paired end read  example_sequence is the name of the output file