Workflow Designer Documentation v. 1.17.0
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  • Convert "seq/qual" Pair to FASTQ

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This workflow allows This workflow allows to add PHRED quality scores to the sequence and save output to Fastq. For example, one can read a Fasta file, import PHRED quality values from corresponding qualities file and export the result to Fastq.
To execute the workflow do the following:

  1. Select "Sequence Reader" task and specify source file(s) at "URL" field in the Property Editor.
  2. Select "Import PHRED qualities" task and specify URL to the quality file. Usually such files have .qual extension.
  3. Launch the schema with pressing Ctrl+R shrotcut.

After running the workflow, target fastq file will appear in the same folder as the source file, with the same name but diffrent extension.

Tip
titleHow to Use This Sample

If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation.

Workflow Sample Location

The workflow sample "Convert "seq/qual" Pair to FASTQ" can be found in the "Conversions" section of the Workflow Designer samples.

Workflow Image

The workflow looks as follows:

HTML
<center>
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  <img src="/wiki/download/attachments/16122704/Convert seq-qual Pair to FASTQ.png"/>
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</center>
Workflow Wizard

The wizard has 2 pages.

  1. Input Sequence(s): On this page you must input sequences(s). 

    HTML
    <center>
  <br>
  <img src="/wiki/download/attachments/

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  1. 16122704/Convert seq

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  1. -qual Pair to FASTQ_1.png"/>
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</center>

  2. Convert "seq/qual" Pair to FASTQ: On this page you can modify converting and output settings. 

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    <center>
  <br>
  <img src="/wiki/download/attachments/16122704/Convert seq-qual Pair to FASTQ_2.png"/>
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</center>

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titleHow to Use This Sample

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  1. The following parameters are available:
    PHRED inputPath to file with PHRED quality scores.
    Quality typeChoose method to encode quality scores.
    File formatQuality values can be in specialized FASTA-like PHRED qual format or encoded similar as in FASTQ files.
    Result fileLocation of output data file. If this attribute is set, slot "Location" in port will not be used.
    Accumulate resultsAccumulate all incoming data in one file or create separate files for each input.In the latter case, an incremental numerical suffix is added to the file name.