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:
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The following parameters are available:
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Short reads — each added short read is a small DNA sequence file. At least one read should be added.
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The Aligning Short The Map NGS Reads with UGENE Genome Aligner has no limitation on short reads length. |
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- Use GPU-optimization — use an openCL-enabled GPU during the alignment (the corresponding hardware should be available on your computer). This option was available until v44.
- Align reverse complement reads — use both: a read and its reverse complement during the alignment.
- Use “best”-mode during the alignment — report only about best alignments (in terms of mismatches).
- Omit reads with qualities lower than — omit all reads with qualities lower than the specified value. Reads that have no qualities are not omited.
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