Workflow Designer Documentation v. 1.21.0
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  • Trim and Align Sanger Reads

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The workflow does the following things:

1) Reads a set of Sanger sequencing reads from ABI files.
2) Trims ends of the reads by the quality value.
3) Filter the short trimmed reads.
4) Aligns the filtered trimmed reads to a reference sequence.

You can change the workflow parameters:

1) Quality threshold for the trimming.
2) Minimum read length. If length of a trimmed read is less than the minimum value than the read is filtered.

The output data are:

1) Multiple sequence alignment file. The first sequence of the alignment is the reference and other ones are the reads.
2) Annotated reference sequence file. The annotations are the aligned reads.

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 "Trim and Align Sanger Reads" can be found in the "Sanger Sequencing" section of the Workflow Designer samples.

Workflow Image

The opened workflow looks as follows:

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/16121890/Trim and Align Sanger Reads.png"/>
  <br> 
</center>
Workflow Wizard

The wizard has 4 pages.

  1. Reference Sequence: On this page you must input reference sequence.  

    HTML
    <center>
  <br>
  <img src="/wiki/download/attachments/16122743/Trim and Align Sanger Reads_1.png"/>
  <br> 
</center>
  2. Input Sanger Reads (ABI Files): On this page you must input ABI file(s).  
    HTML
    <center>
  <br>
  <img src="/wiki/download/attachments/16122743/Trim and Align Sanger Reads_2.png"/>
  <br> 
</center>
  3. Trimming and Filtering: On this page you can modify trimming and filtering settings.  
    HTML
    <center>
  <br>
  <img src="/wiki/download/attachments/16122743/Trim and Align Sanger Reads_3.png"/>
  <br> 
</center>

    The following parameters are available:

    Quality thresholdQuality threshold for trimming.
    Min LengthToo short reads are discarded by the filter.

  4. Results: On this page you can modify output files settings.  

    HTML
    <center>
  <br>
  <img src="/wiki/download/attachments/16122743/Trim and Align Sanger Reads_4.png"/>
  <br> 
</center>