Example 4: Identifying plasmid contigs

Example workflow for finding plasmids in bacterial assembly (Illumina)

1. Create Contiguity-CAG using the command-line or GUI.

2. Load CAG by selecting “Load Assembly” from the “File” menu.

3. Generate sequence alignment by selecting “Create comparison” from “File” menu and selecting the FASTA file of a reference.

4. View the graph by selecting “View assembly” from the “View” menu, select filter from the drop down menu next to “Contigs to view” and then click “Ok”.

5. Too add contigs that may be shared by the plasmid and chromosome choose “Select all” from the tools menu and then select “Find paths” and click “Ok”.

6. Order contigs so that contigs that share an edge are adjacent, there will be multiple ways to order contigs. Duplicate contigs where necessary by right-clicking on the contigs and selecting duplicated form the context-driven menu.

7. Create scaffolds of the potential plasmid by selecting “Write to FASTA” from the “Tools” menu.

8. These scaffolds can then be used to design primers to confirm presence and arrangement of contigs of the plasmid.