Assisted assembly or reference-assisted assembly is a type of Whole Genome Shotgun Assembly in which a known genome (called a reference genome) is used as a reference for creating or improving a new assembly.
Assisted assembly is an alternative to de novo assembly. It is useful in cases where the coverage of the new assembly is too low to guarantee a high-quality de novo assembly. Such a low coverage may result from a desire to save money on sequencing. On the other hand, sometimes a genome may not need to be sequenced at high coverage: some assemblies are sequenced simply for the purpose of aligning with other genomes to look at gene differences. In this case, sequencing at low read coverage is acceptable and a good financial decision.
The general strategy of assisted assembly is to use the reference genome to "validate" particular reads, links, and alignments in the input reads, guaranteeing that they are accurate. These validations can lower the stringency (e.g. the use of single links) and improve both read usage and long range connectivity.
Arachne usually performs de novo assembly, but it is also capable of assisted assembly. The main module that performs assisted assembly is AssistMain. AssistMain calls the modules MakeLookupTable and QueryLookupTable to generate a lookup table of alignments between the input reads and the reference genome.