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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-02-10

AUTHORS

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

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. More... »

PAGES

8365

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/srep08365

DOI

http://dx.doi.org/10.1038/srep08365

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1034123211

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25666585


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28 RAST (Rapid Annotation using Subsystem Technology) annotation engine
29 RAST algorithm
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36 annotation job
37 annotation pipeline
38 annotation protocol
39 archaeal genomes
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47 custom features
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