If your workflow includes the Preassembly Options screen, you can adjust the parameters used for running pre-assembly scans. There are two versions of this screen. This topic describes the used for long-read workflows. If following any other type of workflow, instead see Preassembly Options for all other workflows.

  • Expected genome length – De novo long read assemblies are currently limited to genomes <15 mb in size.

  • Choose between Assemble all reads and Use subset of reads (recommended). If you choose the latter, you must also enter the Desired depth of coverage of final assembly. We recommend keeping the default of 100 times depth of coverage for optimal results. You will also need to specify whether you want SeqMan NGen to Use the longest reads in data set to achieve depth or Use the first n reads in data set to achieve depth.
  • If you wish to correct the longest, higher-quality reads and assembly only those corrected reads, check the box next to Run a first-pass correction assembly.

If desired, press the Advanced Assembly Options button to access additional options. A two-tabbed dialog opens. See Alignment tab and Layout tab for descriptions.

Click Next > to proceed to the next wizard screen or < Back to return to the previous screen.

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