Note: This topic is not applicable to BAM-based projects.
SeqMan Pro provides default pre-assembly and assembly options for each of its assembly methods, Pro and Classic, including end trimming, and removing contaminants, vector, and repetitive sequences.
For some projects, you may want to adjust these parameters. To access them, click the Options button from the Unassembled Sequences window to access the Preassembly and Assembly Options dialog. Alternatively, select Project > Parameters and then click on Preassembling from the list on the left.
For more information on each of the pre-assembly tasks SeqMan Pro offers, see the following topics: End Trimming, Removing Vector Sequences, Removing Contaminant Sequences, and Handling Repeated Sequences.
(above) Classic Pre-Assembly Options, (below) Pro Pre-Assembly Options
•Select Trim sequence ends if you wish to remove poor quality ends of sequence reads as specified by the current End Trimming parameters.
•Select Scan for vector if you wish to remove contaminating vector sequence. In order to select this option, the vector(s) must first be selected. See Removing Vector Sequences for details.
Note: For optimized assembly, we strongly recommend scanning for the vector sequence(s).
•Select Remove contaminant sequences if you wish to remove sequence containing the specified contaminant DNA. This command is only operational once you’ve specified known contaminant DNA(s) by selecting Project > Contaminant Seqs.
•For Classic Assembler only, choose between Optimize sequence assembly order and Use sequence entry order. The former choice is considerably faster.
o Select Optimize sequence assembly order to optimize the assembly process. This option is more likely to assemble contigs accurately than the Use sequence entry order option. If you have identified known repeated DNA, then selecting this radio button will also make SeqMan Pro assemble repetitive sequences last to avoid bias.
o Select Use sequence entry order to use sequences in the order listed in the Unassembled Sequences window.
•If desired, check Don’t add single sequence contigs. When checked, any sequence that does not meet the criteria to align with another sequence will remain in the Unassembled Sequences window. If left unchecked, any single sequences are moved to the Project Summary window as a single-sequence contig.
Note: After assembly, the Unassembled Sequences window will disappear from view. To reopen the window and view any single sequence contigs, select Sequence > Add.
•For Classic Assembler only, you may also wish to check Don’t add new contigs. This prevents the creation of new contigs when new sequences are added to an existing assembly, but do not meet the criteria to enter an existing contig. If unchecked, sequences added to an assembly may join together to form contigs unrelated to the prior assembly.
Note: If there are no existing contigs, SeqMan Pro ignores this checkbox.
After choosing the desired options:
•Click Scan Selections to perform the selected operations immediately, but only for sequences highlighted in the Unassembled Sequences window.
•Click Scan All to perform the operations on all sequences.
•Click Scan Later to postpone the operations until clicking the Assemble button.
Any sequence trimming updates the “Limits” column in the Unassembled Sequences window.