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

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. United States National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Service [HHSN272201400027C]; United States Department of Energy, DOE Systems Biology Knowledgebase [DE-AC02-06CH11357]; United States National Science Foundation [CNS-1305112]; Experimental and Computational Determination of Microbial Genotypes and Phenotypes [MCB-1330800]; National Aeronautics and Space Administration through the NASA Astrobiology Institute [NNA13AA91A] We thank Emily Dietrich for her helpful comments. This work was supported by the United States National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Service [Contract No. HHSN272201400027C]; the United States Department of Energy [DE-AC02-06CH11357], as part of the DOE Systems Biology Knowledgebase; R.A.E. was supported by United States National Science Foundation Grants grants II-EN: Computational Enhancement of Analytical Metagenomics Systems CNS-1305112, and Experimental and Computational Determination of Microbial Genotypes and Phenotypes MCB-1330800; and G.J.O. was supported by the National Aeronautics and Space Administration through the NASA Astrobiology Institute under Cooperative Agreement No. NNA13AA91A issued through the Science Mission Directorate. United States Department of Energy: National Institute of Allergy and Infectious Diseases.