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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.


Matthew Vaughn

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.


    • 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