Assemble sequences

This section describes how to assemble a number of sequence reads into a contig without the use of a reference sequence (a known sequence that can be used for comparison with the other sequences, see Assemble to reference sequence). To perform 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 (Image assemble)

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 De Novo Assembly (Image assemble) tool under De Novo Sequencing (Image de_novo_sequencing) in the Toolbox.

When the sequences are selected, click Next. This will show the dialog in figure 18.6

Image assemblestep2
Figure 18.6: Setting assembly parameters.

This dialog gives you the following options for assembling:

If you have chosen to "Trim sequences", click Next and you will be able to set trim parameters (see Automatic trimming parameters).

Click Next if you wish to adjust how to handle the results. If not, click Finish.

When the assembly process has ended, a number of views will be shown, each containing a contig of two or more sequences that have been matched. If the number of contigs seem too high or low, try again with another Alignment stringency setting. Depending on your choices of output options above, the views will include trace files or only contig sequences. However, the calculation of the contig is carried out the same way, no matter how the contig is displayed.

See View and edit contigs on how to use the resulting contigs.