Note: This topic is not applicable to BAM-based projects.
If you obtain new data for an assembly project, you may either add the new sequences to your existing assembly project, or you may start from scratch and assemble both old and new data all together.
Adding new data to an existing project maintains any edits and trim adjustments you may have made to your assembly project. Assembling from scratch will lose all the edits and trim adjustments but may generate a better assembly.
If you plan to assemble collections of sequence data more than once or in more than one project, you may create a File of Filenames for each collection of data that includes the quality trimming and vector trimming information.
When adding new data to an existing project, consider the following:
•To prevent SeqMan Pro from creating new contigs, check Don’t add new contigs from the Preassembly and Assembly Options dialog. New data will then either be assembled into existing contigs, or, if they do not meet the current assembly criteria, will remain in the Unassembled Sequences window.
•If you want to prevent the new sequences from assembling into one or more existing contig, lock the contig(s) before assembling the new sequences.
•You may not assemble new sequences into a project if any unlocked contigs contain suggested conflicts. If you attempt to assemble in that circumstance, SeqMan Pro displays the message: “Cannot assemble: X contigs with suggested splits are unlocked. Do you wish to cancel the assembly, continue by canceling the suggested splits, or continue by locking contigs with suggestions?”
o Cancel Assembly aborts the assembly.
o Cancel Suggestions works as if you had selected Contig > Cancel Suggestions. After clicking this, any numbers appearing in the “Conflict Splits” column of the Project Summary window reverts to “?”.
o Lock Contigs locks all contigs with suggested splits, and then continues with the assembly. If you click this, the sequence(s) you are assembling into the project will not be added to any of the locked contigs.