Assembly
How to upload FASTA files into KBase.
An assembly file is a single file containing one or more contiguous DNA sequences in FASTA format. It can be uploaded to KBase from your local computer (with file extension .fasta, .fna, .fa, or .fas) or directly from a publicly accessible FTP or HTTP URL.
“Assembly” is the KBase data type for assembled, unannotated DNA sequence contigs. If you want to upload annotated sequences in GenBank or GFF format, please see the Genome page.

Importing a FASTA formatted assembly file from your computer

For this example, we will use an Escherichia coli K12 MG1655 assembly file from NCBI as the source: GCF_000005845.2_ASM584v2_genomic.fna.gz
Download that file to your computer. Next open the Import tab within the Data Browser and drag the assembly file into the Staging Area.
Open the Select a format pulldown menu to the right of the filename in your Staging Area under the Import As... column select “Assembly.”
Now click the import icon to the right of “Assembly”. The data slide-out will close and an app called “Import FASTA File as Assembly from Staging Area” will be added to your Narrative.
Notice that the name of the gzipped Assembly file is already filled in, as is a suggested name for the Assembly data object that will be created by the import (you can change the Assembly object name). Adjust the minimum contig length if needed and then click the green "Run" button to start the import. When the import is finished, your Data Panel will update to show the new Assembly object, and a report will appear in the import app cell.

Drag & Drop Limitations

The drag & drop option from your local computer works for many files, but there is a size limit that depends on your computer and browser. For larger files (around 20GB), use Globus Online transfer.

Bulk Import

Assemblies can be imported as one of the supported bulk import types. You can select multiple assemblies simultaneously from the staging area to import them at once. See the bulk import section of the guide to importing data into the Narrative.

Import an Assembly from other sources

In the Staging Area, beneath the box for Drag & Drop, are other options for getting data. You can import data into your KBase workspace using Globus, or by supplying a URL for a publicly accessible FTP location, Google Drive, Dropbox, or a direct HTTP link. Options for adding data to your Staging Area are described here.

Transfer assemblies from JGI

If you are a JGI user, you can transfer public genome reads and assemblies (as well as your private data and annotated genomes) from JGI to your KBase account—see this page for instructions.
Last modified 2mo ago