Understanding Assembly Reconciliation
What is assembly reconciliation?
A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. As a consequence, it is common practice to produce multiple assemblies using different assemblers/parameters, then select the best one for public release. A more compelling idea is to merge multiple assemblies with the intent to produce a higher quality consensus assembly, which is the objective of assembly reconciliation.