De Novo Assemble

Before merging forward and reverse strand it is necessary to set the read direction of the traces. Select all traces of one direction by using the search option and click on Sequence and Set read direction. Then choose the right direction according to the selected primer in the pop-up window. Do the same for the other direction.

Now select all raw sequences. Right click and select De Novo Assemble.

In the pop-up window, enter the part of the file name that the forward and reverse sequences of a sample have in common (CaBOL-ID) so that they can be put together.

Enter the settings under Options as shown in the illustration. Close both windows with OK.

The raw sequences are now assembled (i.e. forward and reverse sequence are superimposed), and the Assemblies are placed in a new sub-folder CaBOL Assembly in the left;

Open the Assembly Report in the CaBOL Assembly folder and click on the Number of not assembled traces (if any): the raw sequences will be selected automatically. Repeat the assembly as before with only the selected sequences, but this time with the Not trim option .

Cleanup:

1. Move raw sequences that still could not be assembled into a new sub-folder Faulty.
2. Move assembled sequences into the folder Assemble.