If you are working with Sanger data, SeqMan Ultra serves as an application for performing and analyzing Sanger assemblies. If you are working with NGS data, SeqMan Ultra is a workflow launcher for the SeqMan NGen assembler, and the place to perform downstream analysis after assembly.
SeqMan Ultra can be used for downstream analysis of the consensus, features, and other components using a wide range of views and reports. BAM alignment files are not editable, but SeqMan Ultra can be used to edit .sqd formatted assemblies.
Assembly information is summarized in SeqMan Ultra’s tabular reports and graphical views. The Strategy view graphically summarizes the position and orientation of every constituent sequence in a contig or contig scaffold and allows you to easily assess the coverage in your assembly. If coverage seems unsatisfactory, you can add more sequences and reassemble, or you can use the primer walking feature to drive the closure of gaps or to fill in low coverage areas. The Alignment view gives you a more detailed picture of the assembly, and allows you to edit constituent sequences, override the called consensus, review underlying trace or flowgram data, add new features, restore previously trimmed data, and adjust alignments. You may also evaluate putative variants identified by SeqMan NGen, which uses an exceptionally accurate variant-calling algorithm. You can also force contigs to join, or split a contig into two or more segments. Once you are satisfied with your assembly, you may save your project, export the data, or merge contigs with those imported from previous assembly projects.
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