CG-Pipeline NM data
A computational genomics pipeline for prokaryotic sequencing projects
Motivation: New sequencing technologies have accelerated research  on prokaryotic genomes and have made genome sequencing  operations outside major genome sequencing centers routine.  However, no off-the-shelf solution exists for the combined assembly,  gene prediction, genome annotation, and data presentation necessary  to interpret sequencing data. The resulting requirement to invest  significant resources into custom informatics support for genome  sequencing projects remains a major impediment to the accessibility  of high-throughput sequence data.  Results: We present a self-contained, automated high-throughput  open source genome sequencing and computational genomics pipeline  suitable for prokaryotic sequencing projects. The pipeline has  been used at the Georgia Institute of Technology and the Centers  for Disease Control and Prevention for the analysis of Neisseria  meningitidis and Bordetella bronchiseptica genomes. The pipeline is  capable of enhanced or manually assisted reference-based assembly  using multiple assemblers and modes; gene predictor combining;  and functional annotation of genes and gene products. Because  every component of the pipeline is executed on a local machine with  no need to access resources over the Internet, the pipeline is suitable  for projects of a sensitive nature. Annotation of virulence-related  features makes the pipeline particularly useful for projects working  with pathogenic prokaryotes.  Availability and Implementation: The pipeline is licensed under  the open-source GNU General Public License and available at the  Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/).  The pipeline is implemented with a combination of Perl, Bourne  Shell, and MySQL and is compatible with Linux and other Unix systems.