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 Barcode Splitter

FASTX Barcode Splitter is a component of the FASTX Toolkit de-multiplexes barcoded next-gen sequence data.

Quick Start

  • To use FASTX Barcode Splitter upload your data in FASTQ format and upload a Barcodes file. (It is imperative that the barcode file NOT be terminated with a new line character.)
  • Resources: documentation

Test Data

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

Community Data > iplantcollaborative > example_data > fastx_barcode_splitter_single_end

Input File(s)

Use Barcoded.fq as test data and SomeBarcodes.txt as your barcode file.

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.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect one FASTQ file per barcode as output plus one FASTQ file containing the unmatched sequences.

  • Results for test case
    • Sequences_BC1.fq
    • Sequences_BC2.fq
    • Sequences_BC3.fq
    • Sequences_unmatched.fq

FOR THE EXAMPLE DATA PROVIDED, THERE IS ONLY ONE BARCODE (BC1). THE OTHER FILES WILL BE RETURNED AS ZERO BYTE FILES

Tool Source for App

1 Comment

  1. It would be nice if this tool was modified to handle gzipped FASTQ files as well.