deletions | additions       diff --git a/Genome Assembly and Annotation.md b/Genome Assembly and Annotation.md  index 0345f17..c0c5a9e 100644  --- a/Genome Assembly and Annotation.md  +++ b/Genome Assembly and Annotation.md 
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/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.  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. 
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Finally "X\_cov" shows the average coverage across the genome. For Illumina data we recommend that this number be between ~30X and 100X. Much less than 30X coverage and the quality of any given base in the assembly may come into question. Conversely, too much coverage can reduce the quality of the assembly and require downsampling. **Instructions or reference for downsampling?**  ###Verification of 16S Sequence  Follow the steps described in Section ??, "Making a Phylogenetic Tree" for obtaining and BLASTing performing a BLAST search of  the full length 16s sequence. PhyloSift  Navigate to