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

Thomas Brettin; James J. Davis; Terry Disz; Robert A. Edwards; Svetlana Gerdes; Gary J. Olsen; Robert Olson; Ross Overbeek; Bruce Parrello; Gordon D. Pusch; Maulik Shukla; James A. Thomason; Rick Stevens; Veronika Vonstein; Alice R. Wattam; Fangfang Xia

doi:10.1038/srep08365

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

Thomas Brettin, James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Gary J. Olsen, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D. Pusch, Maulik Shukla, James A. Thomason, Rick Stevens, Veronika Vonstein, Alice R. Wattam, Fangfang Xia

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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.

Original language	English
Article number	8365
Number of pages	6
Journal	Scientific Reports
Volume	5
DOIs	https://doi.org/10.1038/srep08365
Publication status	Published - 10 Feb 2015
Externally published	Yes

Bibliographical note

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/

Keywords

RAST
RAST algorithm
annotation pipelines
Genome annotation
bacterial genomics
archaeal genomics

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10.1038/srep08365Licence: CC BY-NC-ND

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Brettin, T., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., Shukla, M., Thomason, J. A., Stevens, R., Vonstein, V., Wattam, A. R., & Xia, F. (2015). RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Scientific Reports, 5, Article 8365. https://doi.org/10.1038/srep08365

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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.",

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author = "Thomas Brettin and Davis, {James J.} and Terry Disz and Edwards, {Robert A.} and Svetlana Gerdes and Olsen, {Gary J.} and Robert Olson and Ross Overbeek and Bruce Parrello and Pusch, {Gordon D.} and Maulik Shukla and Thomason, {James A.} and Rick Stevens and Veronika Vonstein and Wattam, {Alice R.} and Fangfang Xia",

note = "This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License. The images or other third party material in this article are included in the article{\textquoteright}s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/",

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Brettin, T, Davis, JJ, Disz, T, Edwards, RA, Gerdes, S, Olsen, GJ, Olson, R, Overbeek, R, Parrello, B, Pusch, GD, Shukla, M, Thomason, JA, Stevens, R, Vonstein, V, Wattam, AR & Xia, F 2015, 'RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes', Scientific Reports, vol. 5, 8365. https://doi.org/10.1038/srep08365

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

Abstract

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Keywords

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