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When you select the Tools ‣ DNA Assembly ‣ Align short reads item NGS Data analysis‣ Map reads to reference item in the main menu, the Align Short Reads dialog the Map NGS Reads to Reference dialog appears. Set the Align short reads method parameter the Mapping tool parameter to UGENE Genome Aligner. The dialog looks as follows:

     <img src="/wiki/download/attachments/422772165930891/AligningMAP ShortNGS Reads with UGENE Genome Alignerto Reference.png"/>

The following parameters are available:


Short reads — each added short read is a small DNA sequence file. At least one read should be added.


The Aligning Short The Map NGS Reads with UGENE Genome Aligner has no limitation on short reads length.