Short Reads

Bulk Upload

Uploading large numbers of files, such as sequencing read sets, one at time through the Data Panel in the Narrative Interface can be time-consuming. To address this issue, KBase is expanding its data import functionality to support bulk upload of data, meaning that users can import multiple files simultaneously (or single very large files).

You can find out more about using the new (beta) Bulk Upload interface in the Bulk Upload Guide. The instructions in this Data Upload/Download Guide refer to the uploader accessible from the Data Panel in the Narrative Interface.

Short reads can be used as input for several KBase analyses including the Assemble Contigs from Reads app.

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

Upload short reads from a FASTQ file

  • Choose Short Reads as the data type
  • Click the Next button
  • Select the type of file you want to upload:
    • If paired-end reads, click the PAIRED END READS tab (note that this will prompt you for up to two files; only one is needed if you are uploading an interleaved file)
    • If single-end reads, select the SINGLE END READS tab
  • Click the Select File button(s) to open a file browser allowing you to choose a file from your computer
  • Name the object(s) you are importing
  • Click the Import button
  • After the import process has completed, the appropriate data object will appear in your Data Panel as a SingleEndLibrary or PairedEndLibrary.

Paired-end read import example:

Import Paired Reads

Single-end read import example:

Import Single Reads