Menu Command

Description

Contig Info

Ctrl/Cmd+I

To view detailed information for a selected contig.

Alignment View

To access the Alignment View for a selected contig or scaffold of contigs.

You may also access the Alignment View by double-clicking on the contig name(s) in the Project Summary window. Note that when you choose a contig scaffold or multiple contigs, each contig appears in its own Alignment View window.

Strategy View

To access the Strategy View for a selected contig or scaffold of contigs.

You may also access the Strategy View by double-clicking on the scaffold name(s) in the Project Summary window.

Coverage Report

To generate a Coverage Report for a selected contig or scaffold of contigs.

Structural Variation Report

To view information about structural variation in an assembly built using SeqMan NGen.

Sort

To sort the sequences in a contig from the Alignment View or the Strategy View, you may sort by name or offset.

•      Sort > by Name orders sequences by case-insensitive sequence names.

•      Sort > by Offset (default option) orders sequences by offset from the beginning of the contig.

•      Sort > by Variant (available only from the Alignment View) orders sequences in the aligned column with variant bases to the top of the Alignment View, and without variant bases to the bottom.

The currently selected sort option is marked with a checkmark. If you manually rearrange the sequences by dragging on their names, the checkmark is removed until you choose to re-sort.

Name Contig

To change the names of contigs.

Position Contig

To change the numerical value that specifies the position—relative to other contigs—a contig will assume in the Scaffold Strategy View.

You may also specify a contig’s position by clicking and holding the mouse on the position value and typing a new number into the resulting text box.

Delete Contig/Delete Scaffold

To remove the selected contig(s)/scaffold(s) from the assembly project. SeqMan Pro will ask you to confirm the deletion by clicking OK.

You may also delete contigs/scaffolds by selecting the name of the contig in the Project Summary window, and then pressing the Delete key or selecting Edit > Clear.

Complement Contig

To reverse complement the selected contig(s). The command is active from the Project Summary window, the Alignment View, and the Strategy View.

Lock Contig

To lock the selected contig.

Unlock Contig

To unlock the selected contig.

Reassemble Contig

To reassemble one or more contigs in your project.

Align Contigs

To try joining two or more contigs in your project. For more information on this command, see Aligning Contigs.

Align Contigs End to End

To try joining two or more adjacent contigs in your project when you already know the contig order. For more information on this command, see Aligning Contigs.

Force Join Contigs

To manually join two contigs selected from the Project Summary window.

Extend Contig Ends

To restore sequence ends at the beginning and end of a contig.

Suggest Conflict Splits

To locate regions of an alignment containing consistent patterns of conflicts, which may be candidates for contig splitting.

The sequences searched depend on what item you have selected prior to choosing the command:

Cancel Suggestions

To cancel the suggested splits for the selected contig(s).

Split as Suggested

To split contigs in regions that meet your Conflict Split criteria.

Split at Insertion

To divide a contig manually into two separate contigs at a specific location you choose.

Primer Walk

To perform a primer walk on the selected contigs or sequences.

Save Consensus

To export the consensus sequence(s) for the selected contigs to a separate file or files. Four options are available: Single File, Multiple Files, As Single Sequence, or One Sequence Per Scaffold . See Exporting Consensus Sequences for detailed information.

Export Sequences

To export constituent sequences to a separate file or files.