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] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA.
authors: Thomas
authors: T
authors: Brettin
authors: 1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA.
authors: James J
authors: JJ
authors: Davis
authors: Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA.
authors: Terry
authors: T
authors: Disz
authors: 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.
authors: Robert A
authors: RA
authors: Edwards
authors: 1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA.
authors: Svetlana
authors: S
authors: Gerdes
authors: Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors: Gary J
authors: GJ
authors: Olsen
authors: 1] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA [2] Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
authors: Robert
authors: R
authors: Olson
authors: 1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA.
authors: Ross
authors: R
authors: Overbeek
authors: 1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA.
authors: Bruce
authors: B
authors: Parrello
authors: 1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA.
authors: Gordon D
authors: GD
authors: Pusch
authors: Virginia Bioinformatics Institute, Virginia Tech University, Blacksburg, VA, 24060, USA.
authors: Maulik
authors: M
authors: Shukla
authors: USDA-ARS Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor NY, 11724, USA.
authors: James A
authors: JA
authors: Thomason
authors: 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.
authors: Rick
authors: R
authors: Stevens
authors: 1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA.
authors: Veronika
authors: V
authors: Vonstein
authors: Virginia Bioinformatics Institute, Virginia Tech University, Blacksburg, VA, 24060, USA.
authors: Alice R
authors: AR
authors: Wattam
authors: 1] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA [2] Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
authors: Fangfang
authors: F
authors: Xia
mesh_terms: D058977:Molecular Sequence Annotation / Q000379:methods*; D012984:Software