A computational genomics pipeline for prokaryotic sequencing projects.
BACKGROUND
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.


METHODS
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.
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Andrey O
AO
Kislyuk
Lee S
LS
Katz
Sonia
S
Agrawal
Matthew S
MS
Hagen
Andrew B
AB
Conley
Pushkala
P
Jayaraman
Viswateja
V
Nelakuditi
Jay C
JC
Humphrey
Scott A
SA
Sammons
Dhwani
D
Govil
Raydel D
RD
Mair
Kathleen M
KM
Tatti
Maria L
ML
Tondella
Brian H
BH
Harcourt
Leonard W
LW
Mayer
I King
IK
Jordan
D016950:Bordetella bronchiseptica / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D005845:Georgia; D009345:Neisseria meningitidis / Q000235:genetics; D011387:Prokaryotic Cells; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software