Assembly is normally used to align and merge overlapping fragments of a DNA sequence
to reconstruct the original sequence. The assembly essentially appears as a multiple sequence
alignment of reads (called the contig document) and the consensus sequence of the contig can
be used for the reconstruction of the original sequence.
To assemble Sanger sequencing reads (i.e. forward and reverse reads of the same sequence), firstly select all of the sequences you wish to assemble then click Pre-processing in the toolbar and choose Batch assemble sanger sequences in the dropdown.
If you have selected several groups of reads which are to be assembled separately, you can specify a delimiter and an index at which the identifier can be found in all of the names. Sequences are grouped according to the identifier and each group is assembled separately. If a reference sequence is specified, it is used for all groups. For example:
In the above list of reads, “1” and “2” are the identifiers. To assemble the respective reads, choose 2nd for the Name part and _ (underscore) for the Name separator.
Note that you can check whether your respective reads will be assembled together in the Example at the bottom of the Batch assemble sanger sequences popup window.
Once the options are selected and click Run to begin assembling the contig. Once complete, one or more contigs may be generated and an Assembly Report will also be generated.
To view the assembled contigs, select the Contigs (File type: Contig) and to view the consensus sequence, select the Consensus file (File type: Nucleotide Sequence List).
To view the Assembly Report, select the report and click the Assembly Report tab.
Note: The orientation of fragments will be determined automatically, and they will be reversed.