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

Research output: Contribution to journalArticle

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 languageEnglish (US)
Article number8365
JournalScientific reports
Volume5
DOIs
StatePublished - Feb 10 2015

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Genome
Technology
Software
Archaeal Genome
Bacterial Genomes
Computational Biology
Research Personnel
RNA
Research
Proteins

ASJC Scopus subject areas

  • General

Cite this

RASTtk : A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. / 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, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang.

In: Scientific reports, Vol. 5, 8365, 10.02.2015.

Research output: Contribution to journalArticle

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
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, 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. In: Scientific reports. 2015 ; Vol. 5.
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