Hi All, Does anyone know how MIRA uses 454 paired end information in the assembly? When Newbler assembles, it considers PE info and therefore joins contigs within the assembly to produce both scaffolds and contigs as output. Since PE data can be input to MIRA, I'm just wondering where the PE info eventually go, and whether it's ever used to extend/join contigs, other than being assembled into contigs. Thanks. Cheers, Cleo