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Sci Rep. 2015 Feb 10;5:8365. doi: 10.1038/srep08365.

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

Author information

1
1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA.
2
Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA.
3
1] Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA [2] Department of Computer Science, San Diego State University, San Diego, California, 92182, USA.
4
1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA.
5
Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
6
1] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA [2] Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
7
Virginia Bioinformatics Institute, Virginia Tech University, Blacksburg, VA, 24060, USA.
8
USDA-ARS Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor NY, 11724, USA.
9
1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA [3] Department of Computer Science, University of Chicago, Chicago, Illinois, 60637, USA.

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.

PMID:
25666585
PMCID:
PMC4322359
DOI:
10.1038/srep08365
[Indexed for MEDLINE]
Free PMC Article

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