The pipeline for hybrid assembly. The pipeline for hybrid assembly consisted of primary and secondary assembly steps. In primary assembly, the 454, GAIIx, or SOLiD reads were assembled into contigs with Newbler2.0.01.14, Velvet1.1.04, or Denove2.2, respectively. In secondary assembly, contigs from primary assembly step were merged into consensus genome draft with Phrap(Ver1.090518). The consensus was then used as a reference of E.faecium for further analysis.