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.

Figure 1. RASTtk options that are available on the RAST website (http://rast.nmpdr.org).

A table of options is displayed when the user selects the RASTtk annotation scheme and clicks the checkbox for “Customize”. Individual steps can be turned off and on using the check boxes. Parameters and conditions can be changed or added as needed. Dragging and dropping table rows will change the order of the steps.

Figure 2. The RAST workflow.

Each individual step is bounded by a box, and steps are connected by arrows. New RASTtk steps are indicated by red boxes and arrows. Improvements in the original steps are indicated in red text. Steps that are no longer part of the RASTtk pathway are indicated by gray arrows.