Splitting Contigs to Resolve False Joins

Typically, “false join” regions will show:

•      Consistent patterns of sequence conflicts, just as distinct alleles would

•      Regions of abundant conflicts flanking regions of low-frequency but consistent conflicts

•      Large numbers of inconsistencies in assembly orientation and or location of pairs of forward and reverse reads (if you have paired end sequence data)

You may also have independent information to indicate an erroneous join. By selecting Contig > Split as Suggested splits contigs intelligently so that reads are assigned to the appropriate new contigs based on consistent, if minor, sequence differences.

Note that an alternative approach to eliminating false joins would be to assemble the data with a higher Match Size and / or higher Minimum Match Percentage value, as specified under Assembling parameters.