Reassemble Regions
When problematic areas in contigs (mapping or de novo) are encountered, the Reassemble Regions tool can be used as an alternative to manual editing the sequence. This tool is not always capable of fixing problems in the assembly, but may be worth a try. The Reassemble Regions tool adjusts the read mapping and makes changes in the consensus sequence based on reads in the selected region. Reassembly of only an isolated part of the reads may improve the mapping as reads that potentially could have interrupted the first assembly have been removed. The Reassemble Regions tool is a stand-alone wizard driven action, however, reassembly can also be performed by right clicking on a selected reference/contig.
Subsections