Assembling contigs

GeneStudio's Contig editor includes a contig assembly function.

To assemble contigs

  • Import the sequences you wish to assemble.
  • Press the Assemble button on the toolbar. This will cause the Trim ends dialog to be displayed.
  • Review the trimming options, then press OK to start the assembly. A progress dialog will be displayed during the assembly, and the Contig control panel will be displayed when the assembly is complete.

Note: when you import sequences, a prompt is displayed asking if you want to assemble the imported sequences. Click OK to assemble the sequences right away, or cancel if you wish to import additional sequences and assemble them later.

The Trim ends dialog
The Trim ends dialog box allows you to set trimming options for both the 5' and 3' ends.

End trimming options include:

  • Trim 5' and 3' ends: toggles end trimming for the 5' and 3' end.
  • Fixed cutoff: trims end at a specified sequence position.
  • Automatic: scans the sequence from the 3' or 5' end looking for a given number of Ns in a 20 base window.
    • Low stringency: scan for 4 Ns in a 20 base window.
    • Medium stringency: scan for 3 Ns in a 20 base window.
    • High stringency: scan for 2 Ns in a 20 base window.

Assembly parameters
The Assembly parameters dialog box allows you to set Consensus calling and Segment overlap options.  To view the assembly parameters dialog box, selectAssembly parameters from the Options menu.

Assembly parameters

  • Consensus majority: the percentage of sequences that have an identical base for the column to be considered resolved. By default, this is set to 100%.
  • Segment overlap options:
    • Minimum identity: the minimum percentage of identical bases that two adjacent segments must share to be considered to overlap.
    • Minimum overlap: the minimum number of identical bases that two adjacent segments must share to be considered to overlap.

Note: The consensus majority can be changed at any time, and is applied instantly.  The segment overlap parameters are applied during assembly only.