Assembly data objects contain one or more contiguous DNA sequences that can be used as input for several KBase analyses, including the Annotate Microbial Contigs app.

Assembly files can be uploaded to KBase from files stored on your local computer or directly from an FTP or HTTP URL as one or more FASTA files (with file extension .fasta, .fna, .fa, or .fas).

Importing from a FASTA formatted file from your computer

For this example, we will use an Escherichia coli K12 MG1655 assembly file from NCBI as the source:

After downloading and unzipping the file, navigate to the Import tab in the Data Browser to perform the following steps.

  • Choose Assembly from the data type dropdown menu
  • Click the Next button
  • Select the UPLOAD FROM FASTA FILE tab
  • Select a FASTA file from a directory on your computer
  • Provide a name for the Assembly data object
  • Click the Import button; a cell will appear in the Narrative showing the import status
  • After the import process has completed, an Assembly object will be generated and appear in your Data Panel

Importing from FTP

Another way to import assembly files is by specifying a FTP or HTTP link. For this example, we will import the the same Escherichia coli K12 MG1655 as in the example above using the FTP importer.

Before following the steps below, right click and select “Copy Link Address” on this FTP link for the Escherichia coli K12 MG1655 assembly.

  • Choose Assembly from the data type dropdown menu
  • Click the Next button
  • Select the IMPORT FROM FTP tab
  • Copy and paste the FTP link for the desired FASTA file into the “FTP File” field
  • Provide a name for the Assembly data object
  • Click the Import button; a cell will appear in the Narrative showing the import status
  • After the import process has completed, the Assembly object will appear in your Data Panel