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

Discovery Environment Applications List

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FASTX Trimmer 0.0.14

FASTX Trimmer is used for shortening reads in a FASTQ or FASTA files, often for the purposes of removing barcodes or noise.

Quick Start

Test Data

All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > fastx_trimmer

Input File(s)

Use Barcoded.fq as test data.

Parameters Used in App

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

Use these parameters within the DE app interface:

    • First base to keep - 5
    • Leave other parameters their default values.

Output File(s)

Expect a FASTQ file fastx_trimmer_out.fastq as output.

Related Tutorials

ChIPseq Using the CyVerse Discovery Environment


  1. ★★★★★ awesome script! (by andrese52)

  2. ★★★★★ good and reliable (by dr_richard_barker)

  3. ★★★★★ null (by nareshvasani)

  4. Won't handle gzipped files (i.e. fastq.gz).  Files have to be unzipped prior to using this tool.