Note: This topic is not applicable to BAM-based projects.
SeqMan Pro’s Contig > Align Contigs command is useful if you want to test whether two or more contigs can be joined after either restoring data that has been trimmed or relaxing the criteria for alignment or both. To use this option, select the desired contigs from the Project Summary window, and then select Contig > Align Contigs. SeqMan Pro will perform a series of pairwise comparisons, considering every possible orientation. Individual contigs that meet your new criteria will be joined into one or more new contigs.
To try joining two or more adjacent contigs in your project, instead use Contig > Align Contigs End to End. This option is very useful when you know the relative order of the contigs, as it prevents mis-joining of distant contigs that happen to have the same sequences at the contig ends.
In both cases, realigning contigs is faster than reassembling contigs, as realignment only considers ~1 kilobase at the end of each contig.