Downloading Data

After running an analysis in KBase, you may wish to download the results to your local computer. The Narrative Interface offers the ability to download many of the data types stored in KBase, in various popular formats. Additional data types and output formats will be supported soon.

 

Data Type Available Download Formats
Reads (SingleEndLibrary) FASTA/FASTQ JSON
Reads (PairedEndLibrary) FASTA/FASTQ JSON
ReferenceAssembly JSON
ContigSet FASTA JSON
Genome GenBank (see warning below) JSON
GenomeSet JSON
Pangenome TSV EXCEL JSON
Transcriptome GenBank JSON
ProteomeComparison JSON
Tree JSON
Metagenome JSON
Collection JSON
TaxonomicMatrix JSON
FunctionalMatrix JSON
FBAModel SBML TSV EXCEL JSON
FBA TSV EXCEL JSON
Media TSV EXCEL JSON
PhenotypeSet TSV JSON
PhenotypeSimulationSet TSV EXCEL JSON

Note about downloading genomes with multiple contigs: KBase currently exports Genomes with multiple contigs as separate GenBank (.gbk) files for each contig. Some analysis tools outside of KBase require GenBank flat format (.gbff) files, which are single file representations of all contigs within a Genome. To merge several individual Contig (.gbk) files into a single GenBank flat format (.gbff) file, you can run the following command in a Unix based command line to concatenate these files, replacing “contig1.gbk” etc. with the name of each Contig file and “mergedcontigs.gbff” with the name of the output file:

cat contig1.gbk contig2.gbk contig3.gbk > mergedcontigs.gbff

The KBase Genome uploader can also import GenBank flat format (.gbff) files. For more information about GenBank file formatting, see this textbook chapter.

Download data from your Narrative

    • Locate the data you wish to download in the Data panel under the Analyze tab
    • Hover your mouse over the data object until a “…” symbol appears to the right of its name
    • Click the “…” symbol to reveal advanced options
    • Click the sixth icon from the left, Export / Download Data
    • Select a format for exporting and downloading the data
    • Your data will download to the default downloads folder on your computer

Download

Note to PC users: If downloading a Media, FBAModel, FBA, Pangenome, or PhenotypeSimulationSet file in Excel format, the data will be placed into a zipped folder whose name (or path) can be long, depending on the data object’s name and type. If the folder path becomes too long, Windows may not be able to open it. Try copying or moving the file to a folder or directory that has a shorter path if you encounter problems.

Coming Soon

By popular request, KBase will be rolling out new apps soon that enable Bulk Download of multiple data objects.