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 fastq quality filter 0.0.14

FASTX Quality Filter is based on the FASTX Toolkit. It filters next-gen sequence based on average base quality scores.

Quick Start

  • To use FASTX Quality Filter, upload your data in FASTQ format.
  • Resources: documentation

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_quality_filter

Input File(s)

Use 10K_SRR192294_1.fastq  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:

    • Minimum quality score to keep - 30

Output File(s)

Expect a FASTQ file fastq_quality_filter_out.fastq as output.

Tool Source for App

2 Comments

  1. ★★★★★ i like this tool, it's simple yet useful (by mkhalfan)

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