Push Microbial Assemblies to KBase

You can also transfer genomes assemblies from JGI  to KBase for analysis. Search through the results to identify an organism of interest. Once an organism of interest has been identified:

  • Click the “Download” link under the Resources column

JGI-4

  • Read the JGI Data Usage Policy that appears after entering the download area. This statement varies for different organisms, so be sure to read carefully. After agreeing to the policy, click the “Ok” button to continue to the download page.
  • Open the folder labeled QC and Genome Assembly to access the quality controlled assembly file associated with this organism.
  • Notice that the file name for the assembly file is listed as submission.assembly.fasta and is at the bottom of the list of files.
  • Use the checkboxes to the left of the folders and files to select the assembly file to push to KBase. For assemblies, only those uploaded after December 2013 can currently be pushed to KBase.
  • Select the desired files and click the “Push to KBase” button toward the top of the page. This will open a prompt to sign into KBase with your KBase account credentials.

JGI Select Assembly

Push Email

  • After signing into KBase from this prompt, JGI will place the data in a queue for pushing to KBase. Once the data has been successfully pushed, you will receive email with a link to access the data and place it into an existing Narrative.

Push Email

  • Following this link opens a page within KBase that allows the user to either copy the JGI data into an existing Narrative or launch the Convert Assembly File to Contigs app with this data preloaded.

JGI Data Import Assembly Page

Alternatively, you can access the data you transferred within the Data Panel:

  • Create a new Narrative or open an existing Narrative.
  • The dataset you transferred can be seen in the Narrative Data Panel under the “Shared With Me” tab. The data you have most recently transferred from JGI will be first on the list. With your JGI data in KBase, you can perform other analyses on it and save your results and commentary to share with collaborators.

JGI-GIF

Completing these steps pushes data from the JGI Genome Portal into a KBase Narrative for further analysis. In the future, users will be able to push more data types from JGI to KBase.

If you have any questions about pushing data to KBase from the JGI Genome Portal, please contact KBase support.