Assemble and Annotate Your Genome Sequences

by patricwpadmin

PATRIC now provides genome assembly and annotation services. Through the new PATRIC workspace, users can now upload reads and assemble them.  Users can also annotate their genome sequence starting with either the output of the assembly service or their own sequence files.

NOTE: You must have a PATRIC user account and be logged in to use the services and workspace.


Genome Assembly Service:

The new Genome Assembly Service App can be used to perform an automatic genome assembly using the latest computational tools. Single or multiple assemblers can be invoked to compare results. Resulting assemblies are automatically processed via a collection of analysis tools developed by both PATRIC and the research community. The assembly method attempts to select the best (the smallest number of contigs, the longest average contig length) assembly to suggest to the user. Several assembly workflows or “recipes” are available. These workflows have been tuned and tested to fit certain dataset types or desired analysis criteria such as throughput or rigor. The compute engine’s flexible nature also enables the rapid design and emulation of other popular protocols.  The PATRIC Genome Assembly Service App can be accessed from the Services/Genome Assembly menu item, as shown below.

Assemble_menu4

Genome Annotation Service:

The new Genome Annotation Service App utilizes the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. The original RAST (Rapid Annotation using Subsystem Technology) annotation engine was built 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. RASTtk extends RAST by offering 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. The PATRIC Genome Annotation Service App can be accessed from the Services/Annotate Genome menu item:

Annotate_menu3

Differential Expression Service:

As part of the workspace upgrade we have migrated the capability to upload and transform expression data to a service named “Differential Expression”.  The Differential Expression Service allows users to upload experiment data into their workspace and compare it with other expression data in PATRIC.  This service supports transcriptomics and proteomics data in the form of log ratios, generated by comparing samples, conditions, or time points.

Diff-Exp_menu

Updated Workspace:

We have implemented a new workspace in PATRIC to support the new genome assembly and annotation service apps and other services.  This workspace allows users to upload their data files (e.g., sequence reads, assembled genomes, etc.), run the desired service apps, store the resulting output files, and download the results.  It also provides basic tools for organizing and managing files in the workspace. The private data for existing registered PATRIC users has been migrated to the new workspace.  Non-registered users can create their own private workspace by clicking “Sign Up” in the top-right corner of the PATRIC website. The new workspace supports most of the same functions as the previous workspace, such as group creation.  It does not yet support group comparison. Note that for now, to use the “create group” feature, you will need to be a registered user. An overview diagram of the new workspace is provided below.

workspace_overview_smaller

1. Group folder indicator. The new workspace has folders that are dedicated to specific data types including Genomes, Features, and Experiments.  Users can also add their own custom folders

2. Listing of the groups within the selected folder.

3. Controls for the groups. The controls that are displayed depend on the type and selection of data displayed in (2). Each contol has a label that can be seen by hovering over it with the mouse.

4. Details panel.  Displays additional information about the selected item in (2). Can be toggled on and off by clicking the “i” control in (3).

5. Upload File and New Folder controls.

6. File Upload and Job Service status indicators.  Hovering over either of these provides additional information for interpretation of the status.