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Title: RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

Abstract

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

Authors:
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Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Institutes of Health (NIH) - National Institute of Allergy and Infectious Diseases (NIAID); USDOE U.S. Department of Energy; National Science Foundation (NSF)
OSTI Identifier:
1391665
DOE Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article
Resource Relation:
Journal Name: Scientific Reports; Journal Volume: 5; Journal Issue: 1
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING

Citation Formats

Brettin, Thomas, Davis, James J., Disz, Terry, Edwards, Robert A., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Thomason, James A., Stevens, Rick, Vonstein, Veronika, Wattam, Alice R., and Xia, Fangfang. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. United States: N. p., 2015. Web. doi:10.1038/srep08365.
Brettin, Thomas, Davis, James J., Disz, Terry, Edwards, Robert A., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Thomason, James A., Stevens, Rick, Vonstein, Veronika, Wattam, Alice R., & Xia, Fangfang. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. United States. doi:10.1038/srep08365.
Brettin, Thomas, Davis, James J., Disz, Terry, Edwards, Robert A., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Thomason, James A., Stevens, Rick, Vonstein, Veronika, Wattam, Alice R., and Xia, Fangfang. Tue . "RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes". United States. doi:10.1038/srep08365.
@article{osti_1391665,
title = {RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes},
author = {Brettin, Thomas and Davis, James J. and Disz, Terry and Edwards, Robert A. and Gerdes, Svetlana and Olsen, Gary J. and Olson, Robert and Overbeek, Ross and Parrello, Bruce and Pusch, Gordon D. and Shukla, Maulik and Thomason, James A. and Stevens, Rick and Vonstein, Veronika and Wattam, Alice R. and Xia, Fangfang},
abstractNote = {The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.},
doi = {10.1038/srep08365},
journal = {Scientific Reports},
number = 1,
volume = 5,
place = {United States},
year = {Tue Feb 10 00:00:00 EST 2015},
month = {Tue Feb 10 00:00:00 EST 2015}
}