To use the NextGENe Reads Simulator Tool
1. On the NextGENe main menu, click Tools > Reads Simulator.
The Reads Simulator dialog box opens.
2. In the Input pane, click Add to browse to and select the .fasta reference file from which the synthetic data is being created.
3. In the Output field, you can leave the default value for the location of the output files as is (the default value is the directory path for the input file), or you can click Set to select a different location.
4. Select the options for creating the synthetic data.
Setting | Description |
|---|---|
SOLiD | Select this option to create reads in color-space. |
Paired Reads | Select this option to create paired reads. |
Both Directions | Select this option to create both forward and reverse reads, which by definition, doubles the number of reads and total coverage. If you do not select this option, then only forward reads are created. |
Steps | The value that you enter for this option determines the number of references bases that are between the start of each read. A lower value results in more reads and therefore, greater coverage. |
Error Rate | The Reads Simulator tool can incorporate errors into generated reads. Enter a value in this field to incorporate randomly generated errors, or set the value to “0” to have all the generated reads be an exact match to the reference genome. |
Include Indels | Available only if the Error Rate is > 0. Select this option to include insertion errors and deletion errors in the generated reads. |
Library Size | Available only if Paired Reads is selected. The size of the DNA fragment that is being simulated. |
Random Library Size | Available only if Paired Reads is selected. Select this option to create pairs with random distribution of sizes that are centered based on the library size. For example, if the Library Size is set to 200, read pairs will have a gap size between 100 and 300. Note: If you do not select this option, all paired reads will have an identical library size. |
5. Click OK.
A message opens when the process is completed. A single .fasta file is produced and its name is appended with the phrase “_SimulatedReads.” The file is stored in a folder of the same name as shown in the figure below.
6. Click OK to close the message and return to the Reads Simulator tool.