The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.






Skip to end of metadata
Go to start of metadata


Community rating: ?????

Quick Start

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Shared With Me” -> luj -> variant_calling.

Input File(s)

  • Use directory seqtk_seq_input from the directory above as directory containing sequence data.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input directory to get the output provided in the next section below.

  • Use these parameters within the DE app interface:
    • Select "64" in "quality shift"
    • Check "convert quality to Q33"

Advanced Use

  • The sequence data should be in FASTA/Q format which can also be optionally compressed by gzip.
  • You should select correct quality shift for you data. Default 33 is the most commonly used on current sequencing platforms.
  • Check "convert quality to Q33" to convert fastq file with quality shift 33.
  • You could mask bases with quality lower than a number you select and/or mask bases with quality higher than a number you select.
  • You could select the character masked bases converted to, default to lowercase
  • You could drop sequences with length shorter than a number you select and/or drop comments at the header lines

Output File(s)

Expect a directory named seqtk_seq_output as output directory containing converted sequence files.

Tool Source for App

  • No labels