velveth with -separate option

[leshin]

I just notice that velveth now has a -separate option for paired-read files, so I do not need to create an interleaved single input file with a correct order of left and right reads. But, if I use -separate option for paired-read files, do my two input files still have to be the same order for left and right reads (the first read of two input files are paired, and 2,3,4,..etc)? Will velvet figure out the paired relationship by looking at the sequence ID?

LW