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

     <img src="/wiki/download/attachments/4227721/Aligning Short Reads with UGENE Genome Aligner.png"/>

The following parameters are available:

Reference sequence — DNA sequence to align short reads to. This parameter is required.

Result file name — file in UGENE database format or SAM format (if the box SAM output check), to write the result of the alignment into. This parameter is required.

Prebuilt index — check this box to use an index file instead of a reference sequence. Also you can build it manually.

SAM output — checking this box allows one to save output files in the SAM format. The default format of output files is the UGENE database format (ugenedb).

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

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

Common parameters:

Mismatches allowed — check this box to allow mismatches between the reference sequence and a short read. Select one of the following:

Align options:

Advanced parameters:

Maximum memory for short reads — maximum memory usage for short reads. This parameter allows one to decrease the load on the computer on one side and to increase the computer speed of the task on the other side.

Index parameters:

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

You can choose a temporary directory for saving index files for the reference that will be built during the alignment. If you need to run this algorithm one more time with the same reference and with the same reference fragmentation parameter, you can use this prebuilt index that will be located in the temporary directory.