  Metagenomic studies have primarily relied on de novo assembly for
reconstructing genes and genomes from microbial mixtures. While
reference-guided approaches have been employed in the assembly of single
organisms, they have not been used in a metagenomic context. Here we describe
the first effective approach for reference-guided metagenomic assembly that can
complement and improve upon de novo metagenomic assembly methods for certain
organisms. Such approaches will be increasingly useful as more genomes are
sequenced and made publicly available.
