Hi,

Before reinventing the wheel I wanted to know if somebody knows an exisiting tool to generate paired-end fusion reads (DNA-Seq not RNA-Seq) using always a specific genomic region as origin of the fusion and a random position in the genome as destination (not in a repeated region if possible). Paired-reads don't need to be stranded. But some available tuning parameters such as read length, error rate, inner distance mean, inner distance sd will be great.

edit The breakpoint should be in read 1. And the origin sequence should always has the same length and sequence.

Example : (A = origin and B = destination )

     Breakpoint
        ||
AAAAAAAAABBBBBBBBBBB----------------------BBBBBBBBBBBBBBBBBBB
AAAAAAAAABBBBBBBBBBB-----------------------------BBBBBBBBBBBBBBBBBBB
AAAAAAAAABBBBBBBBBBB------------------------------------BBBBBBBBBBBBBBBBBBB
AAAAAAAAABBBBBBBBBBB-------------------------------------------BBBBBBBBBBBBBBBBBBB

Thanks