skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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:
 [1];  [1];  [2];  [3];  [4];  [5];  [6];  [4];  [4];  [4];  [7];  [8];  [1];  [4];  [7];  [6]
  1. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
  2. Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
  3. Argonne National Lab. (ANL), Argonne, IL (United States); San Diego State Univ., San Diego, CA (United States)
  4. Argonne National Lab. (ANL), Argonne, IL (United States); Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
  5. University of Illinois at Urbana-Champaign, Urbana, IL (US)
  6. Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
  7. Virginia Tech Univ., Blacksburg, VA (United States)
  8. USDA-ARS Lab. at Cold Spring Harbor Lab., NY (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1194128
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 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, III, 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, III, 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, III, 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. https://www.osti.gov/servlets/purl/1194128.
@article{osti_1194128,
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, III, 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 = {2015},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 92 works
Citation information provided by
Web of Science

Save / Share: