Note: This topic is not applicable to BAM-based projects.
The Assemble in Groups feature enables you to assemble certain groups of sequences separately, each into its own contig.
To use this feature, first add your sequences to the Unassembled Sequences window, and define the Preassembly and Assembly options as desired. In the Assembling parameters dialog, select either option: Use Pro Assembler or Use Classic Assembler. Then, click on the Assemble in Groups button from the top of the Unassembled Sequences window:
The Assemble in Groups panel will be displayed in the bottom half of the Unassembled Sequences window:
One of your sequence names will automatically be displayed in the field provided, for you to use as an example. Select the portion of the name that SeqMan Pro should use to identify the sequence as part of a group.
For example, if your sequences have names like 1A_forward.abi, 1B_forward.abi, 1A_reverse.abi, 1B_reverse.abi, etc., then you would want to highlight 1A in the example sequence name so that the forward and reverse reads for the 1A sequence would be assembled together, the forward and reverse reads for the 1B sequence would be assembled together, and so on.
If you are unable to specify a group identifier by highlighting a portion of the name, check the box next to Details to be given to option to enter a group identifier manually:
To define a group identifier manually, enter a regular expression that specifies the group identifier in your sequence names.
After specifying the group identifier, click the Assemble button to begin your assembly.
Samples that have a group identifier will be assembled into contigs named for the group identifier used. For example, the sequences from the example above would assemble into contigs named 1A, 1B, etc.
If you have specified a reference sequence, the reference will go into each contig.
Any reads that do not have a group identifier will not be assembled.