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

Thomas Brettin1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USAJames J. Davis1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USATerry DiszRobert A. Edwards1] 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, USASvetlana Gerdes1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USAGary J. OlsenDepartment of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USARobert Olson1] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA [2] Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USARoss Overbeek1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USABruce Parrello1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USAGordon D. Pusch1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USAMaulik ShuklaVirginia Bioinformatics Institute, Virginia Tech University, Blacksburg, VA, 24060, USAJames ThomasonUSDA-ARS Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor NY, 11724, USARick Stevens1] 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, USAVeronika Vonstein1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USAAlice R. WattamVirginia Bioinformatics Institute, Virginia Tech University, Blacksburg, VA, 24060, USAFangfang Xia1] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA [2] Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA

2015en

ABI

Annotatsiya

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.

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Identifikatorlar

DOI: 10.1038/srep08365

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