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Pesudoassembly is the process of creating a fake assembly of a genome by tiling contigs of a draft genome assembly against a distantly related high-quality (reference) genome using synteny. The overall structure of a pseudoassembly is based on the structure of the reference genome, and may not reflect the actual structure of the genome being pseudoassembled.

CoGe's tool SynMap has an algorithm built in to order and orient contigs of one genome against another genome. This is known as a syntenic path assembly. When this is used in SynMap, the results will contain a link to print out a pseudoassembly. Each contig is "glued" to its neighboring contig using 100 Ns (the ambiguous nucleotide).


Syntenic path assembly and pseudoassembly syntenic dotplots of the Cannabis sativa (marijuana) v. Prunus persica (peach) using SynMap

GEvo analysis of pseudoassembly of Cannabis genome to peach

Screen shot 2011-08-23 at 1.24.34 PM.png

Note that the pseudoassembled contigs in Cannabis are identifiable by orange bars in the background of the Cannabis panel. These orange bars are the 100 Ns used to join neighboring contigs. Results may be regenerated at .