Metassembler is a software package for reconciling assemblies produced by de novo short-read assemblers such as SOAPdenovo and ALLPATHS-LG. The goal of assembly reconciliation, or "metassembly," is to combine multiple assemblies into a single genome that is superior to all of its constituents. By creating Metassembler, we hope to enable researchers to perform assembly reconciliation in a straightforward and efficient fashion, improving the overall quality of genome assemblies. Metassembler is free, open-source software. The code for Metassembler will be released shortly.