deletions | additions       diff --git a/Genome Assembly and Annotation.md b/Genome Assembly and Annotation.md  index 96842ff..49bc9ca 100644  --- a/Genome Assembly and Annotation.md  +++ b/Genome Assembly and Annotation.md 
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###Options  ***Define annotation and describe how it works (just like you did for assembly)***  Note that we are not describing a genome "analysis" here. While genome annotation marks the final step in our  *There are a number of different pipelines available for annotation of bacterial genomes. These include Prokka (\cite{Seemann_2014}), IMG (\cite{Markowitz_2014}), RAST (\cite{Overbeek_2014}), PGAP (\cite{Angiuoli_2008}) and others.  Each of these pipelines has advantages and disadvantages, and each will give slightly different results. Here we recommend RAST since it is web-based, easy to use, returns results within hours, and provides a toolbox for analyzing the results. However, RAST annotations are very difficult to submit to NCBI so we recommend allowing NCBI to re-annotate the genome with PGAP upon submission.