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You can build an index to optimize short reads alignment using UGENE Genome Aligner. To open the Build Index dialog, select the Tools ‣ NGS data analysis ‣ Build index for reads mapping item in the main menu. Set value of the Align the Map short reads method parameter to UGENE Genome Aligner.


     <img src="/wiki/download/attachments/422772365930893/Building Index for UGENE Genome Aligner.png"/>


Reference fragmentation — this parameter influences the amount of parts the reference will be devideddivided. It is better to make it bigger, but it influences the amount of memory used during the alignment.