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Annotate Multiple Microbial Assemblies with RASTtk - v1.073
RAST_SDK

v.0.1.8

By: landml

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Annotate bacterial or archaeal assemblies and/or assembly sets using RASTtk (Rapid Annotations using Subsystems Technology toolkit).

This KBase annotation App (Annotate Multiple Microbial Assemblies uses components from the RAST (Rapid Annotations using Subsystems Technology) toolkit [1,2,3] to annotate prokaryotic assemblies or to perform computations on a set of assemblies so that they are consistent. The newly generated genomes will have the same names as the input assemblies with .RAST appended.

The release versions of the RASTtk component services used in this app are:

The required input is one or more Assembly objects (older Narratives used the term ContigSet object) and/or AssemblySet objects. An Assembly can be generated using any of the Assembly Apps, by importing a FASTA file, or by uploading an .faa file directly from NCBI via FTP (Upload File to Staging from Web) and then importing. AssemblySets are created with the App Build AssemblySet.

Assemblies have three essential metadata fields that must be completed: scientific name, domain, and genetic code. The default genetic code for bacterial and archaeal genomes is genetic code 11, the default domain is bacterial, and the default scientific name is "unknown taxon". All metadata fields are required because they affect conditional parameters in various programs that are being run. The values specified in the App will be used for all Assemblies annotated. KBase annotation supports genetic codes 11 (most bacteria and archaea), 4 for Mycoplasma, and 25. For more information on genetic codes please refer to this NCBI document. Use applicable scientific names if possible.

The App annotates the Assembly-typed objects (sets of contigs) and generates Genome-typed objects with both coding and non-coding features. By definition, an Assembly has no annotation (only sequence) and the default is to select nearly all of the available options. The available annotation features are in the advanced parameters and are discussed in more detail below.

The Default Annotation Pipeline
Clicking "Run" will run the default pipeline. For a typical 2-5 MBp assembly, the default annotation pipeline should take about 5 minutes per assembly. Because this is the first annotation for these assemblies/genomes, the default pipeline for this App consists of the following steps:

Advanced Annotation Options
If you wish to customize the features in your annotation, click the "show advanced options" link. This will display the full set of available annotation options. The "Call features prophage phispy" optionis unchecked because it is slower.

The Results

GUI Output
The GUI output currently consists of three tabs. The "Overview" tab provides basic information on the annotation job, the "Browse Features" tab allows the user to scroll through the features that were called, and the "Browse Contigs" tab provides information on the contigs in the genome. Users can sort on the various types of features. Note that some features will overlap (e.g., "prophage" and "CDS").

Additional Information
For more information on the steps of the default RAStk pipeline please refer to our publication on this (publication forthcoming). For more detailed tutorial information and to explore the additional functionality of RASTtk not currently available in the Narrative interface please refer to http://tutorial.theseed.org.

Team members who developed & deployed algorithm in KBase: Thomas Brettin, James Davis, Terry Disz, Robert Edwards, Chris Henry, Gary Olsen, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon Pusch, Roman Sutormin, and Fangfang Xia. For questions, please contact us.

The authors of RAST request that if you use the results of this annotation in your work, please cite the first three listed publications:

Related Publications


App Specification:

https://github.com/kbaseapps/RAST_SDK/tree/e6d9052ab7ddeeab4c24340ae75276e740bbb3c4/ui/narrative/methods/annotate_contigsets

Module Commit: e6d9052ab7ddeeab4c24340ae75276e740bbb3c4