Assemble to reference sequence

This section describes how to assemble a number of sequence reads into a contig using a reference sequence. A reference sequence can be particularly helpful when the objective is to characterize SNP variation in the data.

To start the assembly:

        select sequences to assemble | Toolbox in the Menu Bar | Molecular Biology Tools (Image lab_work_support) | Sequencing Data Analysis (Image assemblyfolder)| Assemble Sequences to Reference (Image assembletoreference)

This opens a dialog where you can alter your choice of sequences which you want to assemble. You can also add sequence lists.

Note! You can assemble a maximum of 2000 sequences at a time.

To assemble more sequences, please use the Map Reads to Reference (Image assembletoreference) under NGS Core Tools (Image ngsfolder) in the Toolbox.

When the sequences are selected, click Next, and you will see the dialog shown in figure 18.7

Image assembletoreferencestep2
Figure 18.7: Setting assembly parameters when assembling to a reference sequence.

This dialog gives you the following options for assembling:

When the parameters have been adjusted, click Next, to see the dialog shown in figure 18.8

Image assembletoreferencestep3
Figure 18.8: Different options for the output of the assembly.

In this dialog, you can specify more options:

Click Next if you wish to adjust how to handle the results. If not, click Finish. This will start the assembly process. See View and edit contigs on how to use the resulting contigs.