deletions | additions       diff --git a/Genome Assembly and Annotation.md b/Genome Assembly and Annotation.md  index a5be1d5..6449032 100644  --- a/Genome Assembly and Annotation.md  +++ b/Genome Assembly and Annotation.md 
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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}, GLIMMER \cite{Delcher_2007}, 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 convenient 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. Also, we recommend reporting the annotation results from the PGAP annotation annotations  in the genome announcement (for consistency.) Why do we also run a RAST annotation? Because we are impatient and we like to see results right away. We do not like having to wait for the NCBI sumbission process to be completed before we start exploring our data. ###RAST Annotation  Navigate to http://rast.nmpdr.org/ and register a new account. Once you have created an account, log in.