KBase Documentation
  • KBase Documentation
  • KBase Terms & Conditions
  • Getting Started
    • Signing Up and Signing In
      • Step-by-Step Signup Guide
      • Authentication Update
    • Supported Browsers
    • Narrative Quick Start
    • Narrative Interface User Guide
      • Access the Narrative Interface
      • Tour the Narrative Interface
      • Narrative Navigator
      • Create a Narrative
      • Explore Data
      • Add Data to Your Narrative
      • Browse KBase Analysis Tools
      • Analyze Data Using KBase Apps
      • Job Browser
      • Revise Your Narrative
      • Format Markdown Cells
      • Share Narratives
      • Linking Static Narratives to ORCID
      • Access and Copy Narratives
      • Organizations
    • FAQs
  • Manage Your Account
    • Linking Accounts
    • Linking KBase to ORCiD
  • Working with Data
    • Data Upload and Download Guide
      • Data Types
      • Importing Data
        • Bulk Import Limitations
      • Assembly
      • Genome
      • FASTQ/SRA Reads
      • Flux Balance Analysis (FBA) Model
      • Media
      • Expression Matrix
      • Phenotype Set
      • Amplicon Matrix
      • Chemical Abundance Matrix
      • SampleSet
      • Compressed/Zipped Files
      • Bulk Import Specification
      • Downloading Data
    • Searching, Adding, and Uploading Data
    • Filtering, Managing, and Viewing Data
    • Linking Metadata
      • Ontologies and Validated Terms
    • Public Data in KBase
    • Transfer Data with Globus
  • Using Apps
    • Analysis Apps in KBase
      • Assembly & Annotation
      • Comparative Genomics
      • Metabolic Modeling
      • Metagenomics & Community Exploration
      • Data Matrices - Amplicon, Stats
      • Chemical Abundance
      • Expression & Transcriptomics
    • Apps in Beta
  • Running Common Workflows
    • Assembling & Annotating Microbial Genomes
      • FAQ: Assembly and Annotation
    • Comparative Genomics & Phylogenetic Analysis
      • FAQ: Comparative Genomics
    • Metagenomic & Community Analysis
      • FAQ: Metagenomics & Community Analysis
    • Transcriptomic Analysis
      • FAQ: RNA-seq Analysis
    • Constructing Metabolic Models
      • Constructing and Analyzing Metabolic Flux Models of Microbial Communities
      • FAQ: Metabolic Modeling
  • Community Developed Workflows and Tools
    • Functional Annotation
    • Functional and Taxonomic Profiling of MAGs
    • Taxonomy
    • Viral
    • Random Walk with Restart Toolkit
  • Troubleshooting
    • Problems with the User Interface
    • Help Board
    • How to Report Issues
    • Job Errors and Their Meanings
      • Common Job Errors
        • The Job Log
      • Import Job Errors
      • Assembly App Errors
      • Annotation App Errors
      • Functional Genomics App Errors
      • Modeling App Errors
  • Developing Apps
    • The KBase SDK
    • Create a KBase Developer Account
    • KBase GitHub Repository
  • External Links
    • KBase Narrative Interface
    • KBase web site
    • KBase App Catalog
  • kbase.us
Powered by GitBook
On this page
  • Importing reads from your computer
  • Single-end library in FASTQ or SRA format
  • Paired-end library in FASTQ format
  • Importing a reads library from other sources
  • Bulk Import

Was this helpful?

  1. Working with Data
  2. Data Upload and Download Guide

FASTQ/SRA Reads

Formatting and uploading FASTQ and SRA reads files.

PreviousGenomeNextFlux Balance Analysis (FBA) Model

Last updated 1 month ago

Was this helpful?

In KBase, reads from FASTQ and SRA files can be imported to create reads library data objects. The objects will either be a SingleEndLibrary or a PairedEndLibrary. The tools in KBase can then be used to assemble reads into an “Assembly” data object or to align reads to an “Assembly." After uploading and importing reads data, you may want to refer to the documentation about . Reads can also be used in .

Single-end and paired-end reads can be uploaded in FASTQ or SRA format. For FASTQ files, please ensure that your filename ends with the .fastq, .fnq, or .fq file extension. SRA files should have the .sra file extension. The uploader also accepts compressed files in .zip, .gz, .bz2, .tar.gz, .tar.bz2 formats.

Files can be uploaded into your KBase Staging Area from your local computer or directly from a publicly accessible FTP or HTTP URL.

Importing reads from your computer

Single-end library in FASTQ or SRA format

Using a file on your computer, open the . Then drag & drop the single-end library into your Staging Area. Open the pulldown menu to the right of the filename in the Staging Area and select “FASTQ Reads NonInterleaved" or "SRA Reads."

Make sure the correct file type is selected and the checkbox is active, then click "Import Selected". The slide-out Data Browser will close and an app called “Import FASTQ/SRA File as Reads from Staging Area” will be added to your Narrative.

Notice that the name of the Reads Library file is already filled in, as is a suggested Reads Object Name that will be created by the import (you can change that if you like). Adjust the Sequencing Technology and any of the advanced options if needed. Note that this was a metagenomic sample, we would uncheck the box next to Single Genome. When ready, click the green "Run" button to start the import. When the import is finished, your Data Panel will update to show the new SingleEndLibrary object, and a report will appear in the import app cell.

Paired-end library in FASTQ format

Open the pulldown menu to the right of the filename under the Import As... column in your Staging Area and select “FASTQ Reads NonInterleaved” for the first file in the pair. Make sure the correct file type is selected and the checkbox is active, then click "Import Selected". The Data Browser slide-out will close and the “Import FASTQ/SRA File as Reads from Staging Area” App will open.

Notice that the name of the FASTA/FASTQ file is filled in. A suggested Reads Object Name is also created by the import and can be changed.

If the files are two paired file, you will need to select a file for “Reverse/Right FASTA/FASTQ File Path” from the dropdown.

As with the single-end library example, you can make adjustments to the available parameters. Adjust the Sequencing Technology and any of the advanced options if needed. If the file is an interleaved paired-end library, check the box to the right of Interleaved.

When ready, click the green "Run" button to start the import. When the import is finished, your Data Panel will update to show the new PairedEndLibrary object, and a report will appear in the Import App.

Importing a reads library from other sources

Note that directly importing these files into KBase from the web behaves the essentially the same as uploading to the Staging Area and then importing to a Narrative, except the transfer is carried out by the Importer App. Use the link available to directly download the file as if you were going to save it to your computer.

For SRA reads from NCBI, this generally means navigating to the Data access tab of the Run Browser in the NCBI Sequence Read Archive (SRA) for the reads to import, as seen here:

Copy the SRA-download link located under the Name heading and paste the link into the URL input within the Importer App.

Bulk Import

There are two ways that KBase and recognize a paired-end library. A paired-end library can be either two files which typically have the same name and are designated as forward and reverse or a single interleaved file. Interleaved files use an 8-line format where forward and reverse reads alternate.

Open the and drag either one interleaved file or two paired files into the Staging Area.

In the Staging Area, beneath the box for Drag and Drop, there are other options for adding data to your staging area. You can import reads into KBase using , or by supplying a URL for a publicly accessible FTP location, Google Drive, Dropbox, or a direct HTTP link.

If your reads are in a publicly accessible URL, you can bypass the Staging Area and directly import reads into your Narrative using one of these three apps (which you can find in the Apps panel or the ):

For how to search and download or locate download links for SRA sequences, documentation.

FASTQ and SRA reads 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

GenBank SRA
Globus Online
App Catalog
Import SRA File as Reads From Web
Import Single-End Reads From Web
Import Paired-End Reads From Web
see the NCBI Search and Download
the guide to importing data into the Narrative.
Assembly and Annotation
RNA-seq and expression analysis
Import tab within the Data Browser
Import tab in the Data Browser
FASTQ Single-end Library
SRA Single End Library
Paired-end or non-interleaved FASTQ Import
Interleaved FASTQ Import
For this example, SRR18272216, navigate to the Data access tab and copy the SRA-download link under Name and paste the full link into the Import from Web App.