deletions | additions       diff --git a/Genome Assembly and Annotation.md b/Genome Assembly and Annotation.md  index 74efcc1..8cb0bf0 100644  --- a/Genome Assembly and Annotation.md  +++ b/Genome Assembly and Annotation.md 
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###Options  There are a number of different pipelines available for annotation of bacterial genomes. These include Prokka, IMG, RAST, PGAP and others.  ####Prokka + Prokka  Command line based  http://www.vicbioinformatics.com/software.prokka.shtml  ####Integrated + Integrated  Microbial Genomes (IMG) Requires a login and they do the annotation  http://img.jgi.doe.gov/  ####Rapid + Rapid  Annotation using Subsystem Technology (RAST) Web-based, using closed (unknown) algorithms  http://rast.nmpdr.org/  ####Prokaryotic + Prokaryotic  Genome Automatic Annotation Pipeline (PGAAP) Built into NCBI and only accessible upon request  http://www.ncbi.nlm.nih.gov/genome/annotation_prok/