1) Open an existing assembly or create a new SeqMan Pro project.
•To open an existing SeqMan Pro project or SeqMan NGen assembly, select File > Open.
•To open an existing Phrap or Sequencher assembly project, choose File > Import.
•To begin a new project, select File > New.
a) Specify the sequences to assemble and set up the preassembly and assembly options, such as end trimming and scanning for vector. Projects may utilize any combination of supported formats.
b) Review the project parameters and edit them, if desired.
c) Use the buttons at the top of the Unassembled Sequences window to prepare sequences for assembly. Preassembly options include the removal of vector sequence(s), removal of contaminant sequence(s), identification of repetitive sequence(s), automated 5’ and 3’ end trimming, and manual end setting. Removal of vector sequence(s) is strongly recommended when using Sanger data. We also recommend that you accept the default preassembly option allowing SeqMan Pro to optimize the order in which it assembles sequences. To perform the preassembly processes without assembling the data, click Options, and then click Scan All. Otherwise proceed to the next step.
d) Click Assemble from the Unassembled Sequences window to begin the assembly. To assemble certain groups of sequences separately, use the Assemble in Groups option. Results will be displayed in both the Project Summary window (“Untitled.sqd”) and in a new Report window. The Project Summary window shows constituent sequences in the bottom pane and contigs in the upper pane.
2) Use the Alignment View to examine detailed sequence alignments, traces, features, and individual consensus conflicts.
3) Use a Feature Table to view and manage all of the features within your current project. If desired, add features to the consensus sequence.
4) Use the Strategy View to obtain an overview of coverage, conflicts, paired end data consistency, and consensus features for each contig in your assembly.
5) View reports about your assembly, including the Structural Variation Report, the Project Statistics, the Trim Report, the Coverage Report, and Contig Details.
6) Utilize some of the many post-assembly options that SeqMan Pro offers, including Variant discovery, primer walking, editing conflicts and gaps, and BLAST searching.
7) Select File > Save to save the results of your assembly project. You may also save various reports as separate files.